From 0eb7614638376e3b16cf6162c5dc5a88aa6b7982 Mon Sep 17 00:00:00 2001 From: RickGelhausen Date: Mon, 20 Jan 2020 14:20:38 +0000 Subject: [PATCH] fixed bug where the wrong base was assumed for bam files --- scripts/Ribo_seq_occupancy.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/Ribo_seq_occupancy.py b/scripts/Ribo_seq_occupancy.py index 1f53bbe..6c847a8 100644 --- a/scripts/Ribo_seq_occupancy.py +++ b/scripts/Ribo_seq_occupancy.py @@ -73,7 +73,7 @@ def process_ribo(inputFile,occupancy,min_read_len,max_read_len,outputFileS,outpu for read in inFile.fetch(): bit_flag = int(read.flag) # FLAG; chromosome = read.reference_name # chromosome - genomic_position = read.pos # left-most position + genomic_position = read.pos+1 # left-most position cigar = read.cigarstring # CIGAR string [only M and S observed in bacteria] length = len(read.query_sequence) # footprint length