Hello,

I am trying to extract all reads from chromosome 1 (or any other chromosome) from a fastq file. The fastq file I have is from Illumina.

I looked up ShortRead package, but I don't see an example for this in the vignette. 

Could someone give advice ? 

Thanks,

K

A FASTQ file only contains the read sequence, not the alignment, so it isn't possible to sort a FASTQ in this manner. You would have to align first, in which case you would have a sam/bam/cram file that you can easily filter.

Thank you, just realized this was such a noob question.