Using quality filtered fastq files with TopHat

[bob-loblaw]

Hi all,
I want to use tophat with my paired-ends RNA-Seq data, which are in fastq format. The problem however is that after I quality filter my files using the fastx-toolkit, the reads are no longer in the same order in each paired end file and so will not run in tophat. Sorting my reads could prove to be a bit of a challenge too, each PE file is 20gb + with 100 million + reads. I was wondering if anyone had a similar problem and knew of a work around? I was thinking about using the raw data files in tophat (Which to my knowledge are in the proper order) and quality filtering afterward, although I'm not sure how much of an issue that would be?

[dpryan]

It may prove easier to quality filter/trim with a tool that can directly handle paired-end reads. Look into trimmomatic or trim_galore (I find it to be convenient), among likely others.

[bob-loblaw]

It may prove easier to quality filter/trim with a tool that can directly handle paired-end reads. Look into trimmomatic or trim_galore (I find it to be convenient), among likely others.

Great, thanks. I'll look into that.