Trinity - Type Of Reads: ( Cfa, Cfq, Fa, Or Fq )

Question

[Biomonika (Noolean)]

Hi there!

I accidentaly ran Trinity with cfq parameter instead of fq which I believe is what I wanted - fastq with quality scores. I would really like to know what cfq stands for as I tried to google it with no success :/

from Trinity help: --seqType <string> :type of reads: ( cfa, cfq, fa, or fq )

Thanks for suggestions.

Answer 1

[Farhat]

It stands for colorspace fastq, the output from a SOLiD sequencer. For a brief primer check http://marketing.appliedbiosystems.com/images/Product_Microsites/Solid_Knowledge_MS/pdf/CSHL_Fu.pdf

[Biomonika (Noolean)]

Thank you. I had Illumina data, but all with really high quality scores. Can I expect that results will be similiar if I ran it with cfq instead of fq? (Will compare both runs though)

[Farhat]

No, it will be completely nonsensical most likely.