Question: (Closed) Bam to fastq conversion
0
gravatar for banerjeeshayantan
19 months ago by
banerjeeshayantan130 wrote:

I have a bam file from a cancer dataset and I want to convert it to FASTQ to check its quality. So I use this command samtools fastq #bamfile > cancer.fa. I intend to use this fastq file as an input to the FASTQC tool and get an idea about its quality. But these are paired end reads. So how can I get two read files (fastq) separately,(from a bam file) ? Is it ok to proceed with only one fastq file instead of two(for paired end reads) for quality analysis?

next-gen software error • 886 views
ADD COMMENTlink written 19 months ago by banerjeeshayantan130

Hello banerjeeshayantan!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 19 months ago by Sean Davis25k

FASTQC can not handle paired-end data, and thus only works on separate files (treating forward and reverse read as two independent reads)

see also here: Is Paired End analysis possible with FASTQC

ADD REPLYlink written 19 months ago by lieven.sterck5.8k
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2189 users visited in the last hour