From fastq to qseq?

[DarioC]

Hi there,
I received Illumina reads in fastq format from collaborators. The QC pipeline I am using requires qseq format, does anybody know how I could convert back the fastq to qseq?
Thanks!
D

[drio]

qseq contain the raw basecalls (reads) and qualities without any filtering. The best option for you would be to contact the people that pass you the data and ask them to give you the qseq files.

[DarioC]

Fastq files I have are raw reads with Illumina quality scores. I am using the Galaxy Fastx toolkit to trim and filter fastq files (http://hannonlab.cshl.edu/fastx_tool...mmandline.html).

[drio]

By raw I meant that the illumina pipeline did not applied any filtering.

I am not sure how you can go back to the qseq files from the sequence files (fastq). That's why
I was recommending you to ask your source so they can pass you the qseqs.