samtools fastq (bam2fq) producing non-paired reads

[antifolate]

Hello,

I'm trying to produce 2 fastq files from a bam file with

 samtools fastq -1 reads1.fastq -2 reads2.fastq

but the resulting files don't have matching reads. Some reads in reads1 don't have pairs in reads2 and vice-versa. Is there a solution?

Thanks.

[GenoMax]

Are you able to see both reads in the bam file? If it is a small file you could name sort and see if they are there.

[antifolate]

Hi GenoMax,

bam is binary. I don't speak binary. Did you mean the sam file?

[GenoMax]

Something along the lines of "samtools view your_bam". I have a feeling that you may have a file where the reads that did not map may have been discarded. I assume you got this file from someone else?

If that is all you have to work with then you could repair the output files using repair.sh from BBMap like this:

$ repair.sh in1=r1.fq in2=r2.fq out1=fixed1.fq out2=fixed2.fq outsingle=singletons.fq

[antifolate]

You're exactly right; I used

 samtools view -b -F4

to exclude nonmapped reads. Can I tell it to remove both reads if one is removed, or do I have to Perl that up?

[GenoMax]

You're exactly right; I used

 samtools view -b -F4

to exclude nonmapped reads. Can I tell it to remove both reads if one is removed, or do I have to Perl that up?

If you have the R1/R2 files then just use Brian's repair.sh program from BBMap like shown above.

If you want to use samtools then see this thread: https://www.biostars.org/p/111481/ and then use your original command.

[antifolate]

Thanks GenoMax! This command worked for me:

samtools view -f 0x2 bamfile