Question: converting Indel Realigned Bam to fastq
1
gravatar for Iñigo Prada
10 weeks ago by
Iñigo Prada140
Denmark/University of Copenagen
Iñigo Prada140 wrote:

Hi everyone!

My lab is working on an exome-seq pipeline and I have been given the bam files after performing Indel realignment. I want to perform again all the pipeline as sanity check.

I have converted the bam files to fastq using Picard SamtoFastq and when performing the quality control of the fastq files, the plots are not the same, in spite of being similar. Also I am missing 5 millions of reads in respect to the initial fastq files.

Is there way to get the initial fastq files from this Indel Realigned files?

Thanks for reading,

best,

exome-seq next-gen • 211 views
ADD COMMENTlink modified 10 weeks ago by igor3.6k • written 10 weeks ago by Iñigo Prada140
1

Also I am missing 5 millions of reads in respect to the initial fastq files.

did you remove the duplicates ?

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Pierre Lindenbaum91k

Hi Pierre! thank you!

Yeah, I guess that they must have remove duplicates, I will write to the company that did the first analysis and see what is going on.

Thanks!

ADD REPLYlink written 10 weeks ago by Iñigo Prada140
1
gravatar for igor
10 weeks ago by
igor3.6k
United States
igor3.6k wrote:

As Pierre already mentioned, it's possible that duplicates were removed.

You may have also lost reads that did not align and BAM only has aligned reads. You can check for that with samtools idxstats (if there are no unmapped reads, that is the case).

It's possible that only reads mapped to the target regions were retained in one of the steps.

ADD COMMENTlink written 10 weeks ago by igor3.6k

I will check that!

Thanks!

ADD REPLYlink written 10 weeks ago by Iñigo Prada140
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: 480 users visited in the last hour