Do I need to sort a .bam to convert it to fastq?

Question

[bio_elle]

I need to get a .fq file and I have bam files, I am following a code that I found online that sorts it at first

samtools sort -n file.bam > sorted.bam

and then converts it to fastq

samtools fastq sorted.bam > file.fq

Is the sort needed? I think in this case it was used because the data had paired-end reads and sorting by read name makes it so that the files have the mates in the same order, and that can make things easier when using the fastq files (I think???)

But is it needed in single-end data?

Answer 1

[Pierre Lindenbaum]

samtools sort -n file.bam > sorted.bam and then converts it to fastq samtools fastq sorted.bam > file.fq

use "samtools collate" and pipe it into "samtools fastq"

But is it needed in single-end data?

no

[bio_elle]

So with paired-end I can avoid the sort and use

samtools collate file.bam | samtools fastq > file.fq

while with single end I can directly convert to fastq?