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Testing Chip seq implementation

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Xin He edited this page Nov 22, 2018 · 10 revisions

Testing data (single species data)

find sample here and use

fastq-dump --split-3 SRR8060720

Sample used:

samples
  • human1_pe_SRR7968960_1.fastq
  • human1_pe_SRR7968960_2.fastq
  • human2_pe_SRR7968966_1.fastq
  • human2_pe_SRR7968966_2.fastq
  • mouse1_pe_ERR2721212_1.fastq
  • mouse1_pe_ERR2721212_2.fastq
  • mouse2_pe_SRR7873409_1.fastq
  • mouse2_pe_SRR7873409_2.fastq
  • human1_se_SRR8060720.fastq
  • human2_se_SRR8084618.fastq
  • mouse1_se_SRR8098518.fastq
  • mouse2_se_SRR8100057.fastq

Results:

multiqc table

multiqc_report_chipseq

type strategy sample species % Assigned M Assigned
pe conservative human_1 human 70.30% 22.50
pe conservative_without_multimap human_1 human 83.10% 26.60
pe best human_1 human 97.90% 31.30
pe best_without_multimap human_1 human 97.90% 31.30
pe recall human_1 human 98.80% 31.60
pe recall_without_multimap human_1 human 98.80% 31.60
pe permissive human_1 human 99.90% 31.90
pe permissive_without_multimap human_1 human 99.90% 31.90
pe conservative human_1 mouse 0.00% 0.00
pe conservative_without_multimap human_1 mouse 0.00% 0.00
pe best human_1 mouse 6.20% 0.00
pe best_without_multimap human_1 mouse 1.20% 0.00
pe recall human_1 mouse 8.20% 0.00
pe recall_without_multimap human_1 mouse 3.10% 0.00
pe permissive human_1 mouse 15.20% 0.00
pe permissive_without_multimap human_1 mouse 9.20% 0.00
pe conservative human_2 human 73.30% 17.60
pe conservative_without_multimap human_2 human 86.40% 20.80
pe best human_2 human 97.90% 23.50
pe best_without_multimap human_2 human 97.90% 23.50
pe recall human_2 human 98.70% 23.70
pe recall_without_multimap human_2 human 98.70% 23.70
pe permissive human_2 human 99.90% 24.00
pe permissive_without_multimap human_2 human 99.90% 24.00
pe conservative human_2 mouse 0.60% 0.00
pe conservative_without_multimap human_2 mouse 0.70% 0.00
pe best human_2 mouse 3.80% 0.00
pe best_without_multimap human_2 mouse 1.60% 0.00
pe recall human_2 mouse 6.40% 0.00
pe recall_without_multimap human_2 mouse 4.00% 0.00
pe permissive human_2 mouse 15.40% 0.00
pe permissive_without_multimap human_2 mouse 11.70% 0.00
pe conservative mouse_1 human 2.00% 0.00
pe conservative_without_multimap mouse_1 human 2.90% 0.00
pe best mouse_1 human 9.20% 0.00
pe best_without_multimap mouse_1 human 8.90% 0.00
pe recall mouse_1 human 11.90% 0.00
pe recall_without_multimap mouse_1 human 11.50% 0.00
pe permissive mouse_1 human 16.70% 0.00
pe permissive_without_multimap mouse_1 human 16.00% 0.00
pe conservative mouse_1 mouse 71.80% 8.40
pe conservative_without_multimap mouse_1 mouse 85.60% 10.00
pe best mouse_1 mouse 93.30% 10.90
pe best_without_multimap mouse_1 mouse 93.30% 10.90
pe recall mouse_1 mouse 96.50% 11.30
pe recall_without_multimap mouse_1 mouse 96.50% 11.20
pe permissive mouse_1 mouse 99.70% 11.60
pe permissive_without_multimap mouse_1 mouse 99.70% 11.60
pe conservative mouse_2 human 0.20% 0.00
pe conservative_without_multimap mouse_2 human 2.20% 0.00
pe best mouse_2 human 7.30% 0.00
pe best_without_multimap mouse_2 human 6.50% 0.00
pe recall mouse_2 human 8.50% 0.00
pe recall_without_multimap mouse_2 human 7.50% 0.00
pe permissive mouse_2 human 9.70% 0.00
pe permissive_without_multimap mouse_2 human 8.40% 0.00
pe conservative mouse_2 mouse 67.00% 19.70
pe conservative_without_multimap mouse_2 mouse 81.50% 23.90
pe best mouse_2 mouse 92.70% 27.20
pe best_without_multimap mouse_2 mouse 92.60% 27.20
pe recall mouse_2 mouse 96.90% 28.50
pe recall_without_multimap mouse_2 mouse 96.90% 28.50
pe permissive mouse_2 mouse 100.00% 29.40
pe permissive_without_multimap mouse_2 mouse 99.90% 29.40
se conservative human_1 human 63.20% 22.70
se conservative_without_multimap human_1 human 83.60% 30.00
se best human_1 human 96.60% 34.70
se best_without_multimap human_1 human 96.60% 34.70
se recall human_1 human 96.80% 34.80
se recall_without_multimap human_1 human 96.80% 34.80
se permissive human_1 human 99.80% 35.80
se permissive_without_multimap human_1 human 99.80% 35.80
se conservative human_1 mouse 4.80% 0.00
se conservative_without_multimap human_1 mouse 6.00% 0.00
se best human_1 mouse 8.80% 0.00
se best_without_multimap human_1 mouse 8.30% 0.00
se recall human_1 mouse 10.00% 0.00
se recall_without_multimap human_1 mouse 9.50% 0.00
se permissive human_1 mouse 12.50% 0.10
se permissive_without_multimap human_1 mouse 11.20% 0.10
se conservative human_2 human 67.20% 25.30
se conservative_without_multimap human_2 human 84.10% 31.70
se best human_2 human 95.20% 35.90
se best_without_multimap human_2 human 95.10% 35.90
se recall human_2 human 97.40% 36.70
se recall_without_multimap human_2 human 97.40% 36.70
se permissive human_2 human 99.80% 37.60
se permissive_without_multimap human_2 human 99.80% 37.60
se conservative human_2 mouse 0.10% 0.00
se conservative_without_multimap human_2 mouse 0.10% 0.00
se best human_2 mouse 4.10% 0.00
se best_without_multimap human_2 mouse 0.30% 0.00
se recall human_2 mouse 5.20% 0.00
se recall_without_multimap human_2 mouse 1.30% 0.00
se permissive human_2 mouse 9.70% 0.00
se permissive_without_multimap human_2 mouse 4.90% 0.00
se conservative mouse_1 human 1.20% 0.00
se conservative_without_multimap mouse_1 human 1.70% 0.00
se best mouse_1 human 2.50% 0.00
se best_without_multimap mouse_1 human 2.10% 0.00
se recall mouse_1 human 3.40% 0.00
se recall_without_multimap mouse_1 human 3.00% 0.00
se permissive mouse_1 human 4.10% 0.00
se permissive_without_multimap mouse_1 human 3.50% 0.00
se conservative mouse_1 mouse 68.80% 17.10
se conservative_without_multimap mouse_1 mouse 92.30% 22.90
se best mouse_1 mouse 93.60% 23.20
se best_without_multimap mouse_1 mouse 93.60% 23.20
se recall mouse_1 mouse 97.80% 24.30
se recall_without_multimap mouse_1 mouse 97.80% 24.30
se permissive mouse_1 mouse 99.50% 24.70
se permissive_without_multimap mouse_1 mouse 99.50% 24.70
se conservative mouse_2 human 1.00% 0.00
se conservative_without_multimap mouse_2 human 1.40% 0.00
se best mouse_2 human 13.00% 0.20
se best_without_multimap mouse_2 human 12.50% 0.20
se recall mouse_2 human 13.50% 0.20
se recall_without_multimap mouse_2 human 12.90% 0.20
se permissive mouse_2 human 18.30% 0.30
se permissive_without_multimap mouse_2 human 17.30% 0.30
se conservative mouse_2 mouse 59.60% 24.90
se conservative_without_multimap mouse_2 mouse 74.80% 31.30
se best mouse_2 mouse 90.60% 37.90
se best_without_multimap mouse_2 mouse 90.60% 37.80
se recall mouse_2 mouse 90.90% 38.00
se recall_without_multimap mouse_2 mouse 90.80% 37.90
se permissive mouse_2 mouse 99.00% 41.40
se permissive_without_multimap mouse_2 mouse 98.70% 41.20

multiqc_report_rna

detail misassign reads 
bash -c grep "assigned" ./se_conservative_mis_mouse_2.log | sort | uniq -c
  16796 assigned due to only one competing filterer!
    459 assigned due to only one filter exist!
     16 assigned due to primart hit CIGAR!
    261 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_permissive_mis_mouse_1.log | sort | uniq -c
   1840 assigned due to number of multimap!
  12464 assigned due to only one competing filterer!
   2455 assigned due to only one filter exist!
    106 assigned due to primart hit CIGAR!
bash -c grep "assigned" ./pe_conservative_mis_human_2.log | sort | uniq -c
      4 assigned Ambigous!
    363 assigned due to only one competing filterer!
      1 assigned due to primart hit CIGAR!
     17 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_recall_mis_mouse_1.log | sort | uniq -c
    255 assigned due to number of multimap!
   3122 assigned due to only one competing filterer!
   1543 assigned due to only one filter exist!
    218 assigned due to primart hit CIGAR!
   2559 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_conservative_mis_human_2.log | sort | uniq -c
      1 assigned Ambigous!
    234 assigned due to only one competing filterer!
      7 assigned due to only one filter exist!
      4 assigned due to primart hit CIGAR!
     93 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_permissive_mis_mouse_2.log | sort | uniq -c
    269 assigned due to number of multimap!
   4111 assigned due to only one competing filterer!
    580 assigned due to only one filter exist!
    154 assigned due to primart hit CIGAR!
    378 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_recall_mis_human_2.log | sort | uniq -c
  15462 assigned due to number of multimap!
    536 assigned due to only one competing filterer!
    577 assigned due to only one filter exist!
     58 assigned due to primart hit CIGAR!
    352 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_conservative_mis_mouse_2.log | sort | uniq -c
    116 assigned due to only one competing filterer!
bash -c grep "assigned" ./se_recall_mis_mouse_1.log | sort | uniq -c
   1840 assigned due to number of multimap!
  11303 assigned due to only one competing filterer!
   2433 assigned due to only one filter exist!
    106 assigned due to primart hit CIGAR!
bash -c grep "assigned" ./se_best_mis_human_1.log | sort | uniq -c
   2210 assigned due to number of multimap!
  33972 assigned due to only one competing filterer!
   3572 assigned due to only one filter exist!
    161 assigned due to primart hit CIGAR!
   1958 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_permissive_mis_human_1.log | sort | uniq -c
   2210 assigned due to number of multimap!
  38709 assigned due to only one competing filterer!
   4274 assigned due to only one filter exist!
    161 assigned due to primart hit CIGAR!
   1958 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_best_mis_human_2.log | sort | uniq -c
  15462 assigned due to number of multimap!
    355 assigned due to only one competing filterer!
    568 assigned due to only one filter exist!
     58 assigned due to primart hit CIGAR!
    352 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_permissive_mis_human_1.log | sort | uniq -c
   3986 assigned due to number of multimap!
   2681 assigned due to only one competing filterer!
    507 assigned due to only one filter exist!
     50 assigned due to primart hit CIGAR!
    327 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_conservative_mis_mouse_1.log | sort | uniq -c
   1589 assigned due to only one competing filterer!
      1 assigned due to only one filter exist!
      1 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_best_mis_human_1.log | sort | uniq -c
   1910 assigned due to number of multimap!
   3155 assigned due to only one competing filterer!
    240 assigned due to only one filter exist!
     27 assigned due to primart hit CIGAR!
    147 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_recall_mis_human_2.log | sort | uniq -c
   1356 assigned due to number of multimap!
    587 assigned due to only one competing filterer!
    326 assigned due to only one filter exist!
     22 assigned due to primart hit CIGAR!
    148 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_recall_mis_human_1.log | sort | uniq -c
   3383 assigned due to number of multimap!
   1895 assigned due to only one competing filterer!
    429 assigned due to only one filter exist!
     41 assigned due to primart hit CIGAR!
    273 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_best_mis_human_2.log | sort | uniq -c
   1356 assigned due to number of multimap!
    500 assigned due to only one competing filterer!
    316 assigned due to only one filter exist!
     22 assigned due to primart hit CIGAR!
    148 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_recall_mis_human_1.log | sort | uniq -c
   2210 assigned due to number of multimap!
  34505 assigned due to only one competing filterer!
   4108 assigned due to only one filter exist!
    161 assigned due to primart hit CIGAR!
   1958 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_permissive_mis_mouse_2.log | sort | uniq -c
   9007 assigned due to number of multimap!
  45591 assigned due to only one competing filterer!
 189246 assigned due to only one filter exist!
    378 assigned due to primart hit CIGAR!
   2465 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_conservative_mis_mouse_1.log | sort | uniq -c
   6694 assigned due to only one competing filterer!
     62 assigned due to only one filter exist!
      3 assigned due to primart hit CIGAR!
bash -c grep "assigned" ./se_best_mis_mouse_1.log | sort | uniq -c
   1840 assigned due to number of multimap!
  10003 assigned due to only one competing filterer!
   2405 assigned due to only one filter exist!
    106 assigned due to primart hit CIGAR!
bash -c grep "assigned" ./pe_recall_mis_mouse_2.log | sort | uniq -c
    250 assigned due to number of multimap!
   3733 assigned due to only one competing filterer!
    547 assigned due to only one filter exist!
    143 assigned due to primart hit CIGAR!
    354 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_permissive_mis_mouse_1.log | sort | uniq -c
    255 assigned due to number of multimap!
   3580 assigned due to only one competing filterer!
   1543 assigned due to only one filter exist!
    218 assigned due to primart hit CIGAR!
   2559 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_recall_mis_mouse_2.log | sort | uniq -c
   9007 assigned due to number of multimap!
  28198 assigned due to only one competing filterer!
 188875 assigned due to only one filter exist!
    378 assigned due to primart hit CIGAR!
   2465 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_conservative_mis_human_1.log | sort | uniq -c
      1 assigned Ambigous!
  22607 assigned due to only one competing filterer!
    277 assigned due to only one filter exist!
     14 assigned due to primart hit CIGAR!
    179 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_conservative_mis_human_1.log | sort | uniq -c
     33 assigned due to only one competinhug filterer!
bash -c grep "assigned" ./pe_best_mis_mouse_1.log | sort | uniq -c
    255 assigned due to number of multimap!
   2917 assigned due to only one competing filterer!
   1525 assigned due to only one filter exist!
    218 assigned due to primart hit CIGAR!
   2559 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_best_mis_mouse_2.log | sort | uniq -c
   9007 assigned due to number of multimap!
  27699 assigned due to only one competing filterer!
 187276 assigned due to only one filter exist!
    378 assigned due to primart hit CIGAR!
   2465 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_permissive_mis_human_2.log | sort | uniq -c
   1356 assigned due to number of multimap!
   1510 assigned due to only one competing filterer!
    327 assigned due to only one filter exist!
     22 assigned due to primart hit CIGAR!
    148 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_best_mis_mouse_2.log | sort | uniq -c
    187 assigned due to number of multimap!
   3543 assigned due to only one competing filterer!
    421 assigned due to only one filter exist!
    116 assigned due to primart hit CIGAR!
    281 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_permissive_mis_human_2.log | sort | uniq -c
  15462 assigned due to number of multimap!
   2958 assigned due to only one competing filterer!
    605 assigned due to only one filter exist!
     58 assigned due to primart hit CIGAR!
    352 assigned due to primary hit min_mismatches!

Wihout multimap


bash -c grep "assigned" ./se_permissive_mis_mouse_1_without_multimap.log | sort | uniq -c
   1840 assigned Ambigous!
  12464 assigned due to only one competing filterer!
   2455 assigned due to only one filter exist!
    106 assigned due to primart hit CIGAR!
bash -c grep "assigned" ./se_conservative_mis_human_2_without_multimap.log | sort | uniq -c
      1 assigned Ambigous!
    234 assigned due to only one competing filterer!
      7 assigned due to only one filter exist!
      4 assigned due to primart hit CIGAR!
     93 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_recall_mis_mouse_1_without_multimap.log | sort | uniq -c
    255 assigned Ambigous!
   3122 assigned due to only one competing filterer!
   1543 assigned due to only one filter exist!
    218 assigned due to primart hit CIGAR!
   2559 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_permissive_mis_mouse_1_without_multimap.log | sort | uniq -c
    255 assigned Ambigous!
   3580 assigned due to only one competing filterer!
   1543 assigned due to only one filter exist!
    218 assigned due to primart hit CIGAR!
   2559 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_best_mis_human_2_without_multimap.log | sort | uniq -c
  15462 assigned Ambigous!
    355 assigned due to only one competing filterer!
    568 assigned due to only one filter exist!
     58 assigned due to primart hit CIGAR!
    352 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_best_mis_human_1_without_multimap.log | sort | uniq -c
   4439 assigned Ambigous!
     51 assigned due to only one competing filterer!
    572 assigned due to only one filter exist!
     57 assigned due to primart hit CIGAR!
    360 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_recall_mis_human_1_without_multimap.log | sort | uniq -c
   4439 assigned Ambigous!
    162 assigned due to only one competing filterer!
    581 assigned due to only one filter exist!
     57 assigned due to primart hit CIGAR!
    360 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_permissive_mis_human_2_without_multimap.log | sort | uniq -c
  15462 assigned Ambigous!
   2958 assigned due to only one competing filterer!
    605 assigned due to only one filter exist!
     58 assigned due to primart hit CIGAR!
    352 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_recall_mis_human_2_without_multimap.log | sort | uniq -c
   1356 assigned Ambigous!
    587 assigned due to only one competing filterer!
    326 assigned due to only one filter exist!
     22 assigned due to primart hit CIGAR!
    148 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_recall_mis_mouse_1_without_multimap.log | sort | uniq -c
   1840 assigned Ambigous!
  11303 assigned due to only one competing filterer!
   2433 assigned due to only one filter exist!
    106 assigned due to primart hit CIGAR!
bash -c grep "assigned" ./se_conservative_mis_human_1_without_multimap.log | sort | uniq -c
      1 assigned Ambigous!
  22607 assigned due to only one competing filterer!
    277 assigned due to only one filter exist!
     14 assigned due to primart hit CIGAR!
    179 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_permissive_mis_human_2_without_multimap.log | sort | uniq -c
   1356 assigned Ambigous!
   1510 assigned due to only one competing filterer!
    327 assigned due to only one filter exist!
     22 assigned due to primart hit CIGAR!
    148 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_conservative_mis_human_1_without_multimap.log | sort | uniq -c
      1 assigned Ambigous!
      1 assigned due to only one competing filterer!
      3 assigned due to only one filter exist!
      3 assigned due to primart hit CIGAR!
     25 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_recall_mis_mouse_2_without_multimap.log | sort | uniq -c
   9007 assigned Ambigous!
  28198 assigned due to only one competing filterer!
 188875 assigned due to only one filter exist!
    378 assigned due to primart hit CIGAR!
   2465 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_best_mis_mouse_2_without_multimap.log | sort | uniq -c
    517 assigned Ambigous!
   1688 assigned due to only one competing filterer!
   1197 assigned due to only one filter exist!
    330 assigned due to primart hit CIGAR!
    816 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_conservative_mis_mouse_1_without_multimap.log | sort | uniq -c
   6694 assigned due to only one competing filterer!
     62 assigned due to only one filter exist!
      3 assigned due to primart hit CIGAR!
bash -c grep "assigned" ./pe_conservative_mis_mouse_2_without_multimap.log | sort | uniq -c
     77 assigned due to only one competing filterer!
      6 assigned due to only one filter exist!
      6 assigned due to primart hit CIGAR!
     27 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_permissive_mis_human_1_without_multimap.log | sort | uniq -c
   4439 assigned Ambigous!
   1372 assigned due to only one competing filterer!
    581 assigned due to only one filter exist!
     57 assigned due to primart hit CIGAR!
    360 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_conservative_mis_mouse_2_without_multimap.log | sort | uniq -c
  16796 assigned due to only one competing filterer!
    459 assigned due to only one filter exist!
     16 assigned due to primart hit CIGAR!
    261 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_permissive_mis_mouse_2_without_multimap.log | sort | uniq -c
   9007 assigned Ambigous!
  45591 assigned due to only one competing filterer!
 189246 assigned due to only one filter exist!
    378 assigned due to primart hit CIGAR!
   2465 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_conservative_mis_human_2_without_multimap.log | sort | uniq -c
      4 assigned Ambigous!
    363 assigned due to only one competing filterer!
      1 assigned due to primart hit CIGAR!
     17 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_best_mis_mouse_1_without_multimap.log | sort | uniq -c
    255 assigned Ambigous!
   2917 assigned due to only one competing filterer!
   1525 assigned due to only one filter exist!
    218 assigned due to primart hit CIGAR!
   2559 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_permissive_mis_mouse_2_without_multimap.log | sort | uniq -c
    517 assigned Ambigous!
   2034 assigned due to only one competing filterer!
   1240 assigned due to only one filter exist!
    330 assigned due to primart hit CIGAR!
    816 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_best_mis_human_2_without_multimap.log | sort | uniq -c
   1356 assigned Ambigous!
    500 assigned due to only one competing filterer!
    316 assigned due to only one filter exist!
     22 assigned due to primart hit CIGAR!
    148 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./pe_conservative_mis_mouse_1_without_multimap.log | sort | uniq -c
   1589 assigned due to only one competing filterer!
      1 assigned due to only one filter exist!
      1 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_recall_mis_human_1_without_multimap.log | sort | uniq -c
   2210 assigned Ambigous!
  34505 assigned due to only one competing filterer!
   4108 assigned due to only one filter exist!
    161 assigned due to primart hit CIGAR!
   1958 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_best_mis_mouse_2_without_multimap.log | sort | uniq -c
   9007 assigned Ambigous!
  27699 assigned due to only one competing filterer!
 187276 assigned due to only one filter exist!
    378 assigned due to primart hit CIGAR!
   2465 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_best_mis_mouse_1_without_multimap.log | sort | uniq -c
   1840 assigned Ambigous!
  10003 assigned due to only one competing filterer!
   2405 assigned due to only one filter exist!
    106 assigned due to primart hit CIGAR!
bash -c grep "assigned" ./pe_recall_mis_mouse_2_without_multimap.log | sort | uniq -c
    517 assigned Ambigous!
   1815 assigned due to only one competing filterer!
   1240 assigned due to only one filter exist!
    330 assigned due to primart hit CIGAR!
    816 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_permissive_mis_human_1_without_multimap.log | sort | uniq -c
   2210 assigned Ambigous!
  38709 assigned due to only one competing filterer!
   4274 assigned due to only one filter exist!
    161 assigned due to primart hit CIGAR!
   1958 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_best_mis_human_1_without_multimap.log | sort | uniq -c
   2210 assigned Ambigous!
  33972 assigned due to only one competing filterer!
   3572 assigned due to only one filter exist!
    161 assigned due to primart hit CIGAR!
   1958 assigned due to primary hit min_mismatches!
bash -c grep "assigned" ./se_recall_mis_human_2_without_multimap.log | sort | uniq -c
  15462 assigned Ambigous!
    536 assigned due to only one competing filterer!
    577 assigned due to only one filter exist!
     58 assigned due to primart hit CIGAR!
    352 assigned due to primary hit min_mismatches!
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