Extract entire reads, rather than aligned segments, from a SAM/BAM file

Question

[gbdias]

Hello,

I am trying to extract long reads from the Blasr .sam output. However, I want to collect the entire raw reads that produced alignments, and not just the aligned segments.

Is there an easy way to do this?

Here is the blasr command I am using:

blasr <reads.fasta> <reference.fasta> -noSplitSubreads -clipping none -sam -out output.sam

[GenoMax]

Grab the read ID's from your SAM file and then pull them out of the original fastq by using filterbyname.sh from BBMap.

Answer 1

[cschu181]

I'd assume that the .bam does not have that information. You'd have to get the read ids and get them from the fastq. Something like the following could work. That's what I used to do to extract paired-end reads (in that case the bam needs to be sorted by name).

grep -A3 -F -f <(samtools view <bamfile> | cut -f 1) <source-fastq> | grep -v "\-\-" > <extracted-reads-fastq>

[gbdias]

Thank you. This strategy worked.

[gbdias]

An alternative I found is to use seqtk. It takes a list of sequence names in a file and extract the sequences from FASTA/Q.

seqtk subseq in.fq name.lst > out.fq