Sort fastq file by coordinate

Question

[Beñat]

I am trying to align my fastq files using Matlab. I need to sort the fastq files by coordinate to use them after in other workflows, but I have problems to do it using bowtie function in Matlab. Do you know any workflow to align and sort the files by coordinate? Thanks for all

[Michael]

Why do you want to run bowtie from Matlab? You can run the aligner directly through the command-line, then use samtools sort to sort the bam file. Using Matlab for this has no specific advantage I could think of. Also fastq files cannot be sorted by coordinate, because they have no coordinates assigned to the reads.

[Beñat]

I am more used to work with Matlab and R than through the command-line, cause I am not used to work with this kind of files Thanks for all!

[John]

As Michael points out, the FASTQ file does not contain where the reads map to, only the read sequence and confidence/quality scores. You can however map the FASTQ to a BAM file (which has the mapping positions relative to a reference genome), then sort the BAM file, then convert that BAM file back to a FASTQ by essentially throwing away the mapping positions (but keeping the reads in the same order).

This sounds really really "odd", and suggests a logical error somewhere along the lines - however we don't know what you want to do with the FASTQ file so it's difficult to say. One thing i can strongly recommend against is using Matlab for this. Matlab is great for certain things, and so is R, but frankly I think this is an excellent opportunity for you to learn a bit of command-line stuff anyway. I doubt you can sort a BAM file from inside Matlab without calling samtools anyway...