Duplicate headers In Sam File
0
0
Entering edit mode
3 months ago
ashenflower ▴ 10

Hello everyone,

I ran bwa mem on a fasta file which was created by concatenating two files of paired reads (I needed to treat them as they were single reads).

Problem is, after mapping I tried to use samtools idxstats to get the number of reads that mapped to each reference sequence, but I got the following error:

[W::sam_hdr_create] Duplicated sequence "A00721:137:HYCH3DSXX:1:1101:3667:1047" in file "aln.sam"

I think this is due to the fact that, if I am not wrong, bwa use only the first part of the headers in the fasta file until the first blank space, so probably paired reads have the same header in the sam file. Unfortunately, I did not realize it before mapping.

Do you know any method which would allow me to solve this problem without re-mapping everything to previously fixed headers?

Thanks!

bwa sam samtools header duplicate • 304 views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode

I needed to treat them as they were single reads

Then you could have aligned them independently.

ADD REPLY

Login before adding your answer.

Traffic: 2187 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6