Question: Bam file with unmapped reads from another genome than reference
0
gravatar for Vca80553
19 months ago by
Vca805530
Stockholm
Vca805530 wrote:

Hello everyone,

I started with bioinformatics 2 weeks ago, so maybe my question is a bit too easy for you, but I don't find any answer for it in other threads. I would appreciate a lot if you could help me out.

This is the case:

I mapped my paired end reads to my viral reference genome (Nextgenmap) and selected those that were mapped and paired (both pairs mapped only). Now I want to filter out, those reads that map also to human DNA (my contaminant). For that, I took the "viral_mapped_paired_end_reads.bam", converted it to fastq (R1 and R2) and mapped it to hg19. In this bam file, I extracted the unmapped paired end. So, I assume that here I have the paired end reads that only mapped to virus before , but not to human now. This bam file has the reads that I want, but unmapped to the human reference genome. No info about the reference viral genome.

Now, how do I continue? I want to do coverage analysis for the viral genome for example. Can I use the unmapped bam file? or do I need to use the viral_mapped_paired_end_reads.bam and filter out the reads that mapped to human? If so, Is it done by extracting reads IDs? Or the IDs change depending on the reference genome?

Thanks a lot

ADD COMMENTlink written 19 months ago by Vca805530
2
gravatar for mastal511
19 months ago by
mastal5112.0k
mastal5112.0k wrote:

Map your reads to hg19 first, remove the reads that map, then align the unmapped reads to the viral genome.

ADD COMMENTlink written 19 months ago by mastal5112.0k

Thanks a lot! I thought it would be faster the other way around, as viral genome is less than 10000 pb. I will do it as you say.

ADD REPLYlink written 19 months ago by Vca805530
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 884 users visited in the last hour