Open GoogleCodeExporter opened 9 years ago
Give me a few days to think about this. Sure, it’s easy to implement, but it
does not have to do anything with adapter trimming per se. But then quality
trimming, which cutadapt also does, is also not really adapter trimming ...
Original comment by marcel.m...@tu-dortmund.de
on 11 Feb 2015 at 1:17
Thanks for considering. I like to use cutadapt as a high quality, tunable
one-stop-shop for preprocessing, including adaptor trimming, quality trimming,
length filtering (post-trim), and (ideally) Casava-filtering. Saves me time not
to have to do each step separately, since I/O is the slow part!
Original comment by jkgren...@gmail.com
on 11 Feb 2015 at 2:20
I understand because that’s how I like to use cutadapt myself ;-). However,
disk I/O shouldn’t be an issue even if you use multiple programs since you
can use a pipe to connect them together, similar to this:
my-casava-filter-program input.fastq | cutadapt -a ADAPTER - > output.fastq
(Assuming here that my-casava-filter-program writes the reads to standard
output.)
Original comment by marcel.m...@tu-dortmund.de
on 11 Feb 2015 at 2:54
True! But there arent any (good) Casava-filtering programs out there (that
I could find). I wrote a quick awk script but Im not really a programmer.
Imight also have to pipe through gzip (twice) to handle the fastq file
de/compression.
Anyway, thanks for considering, its certainly true there are other options!
Original comment by jkgren...@gmail.com
on 11 Feb 2015 at 3:39
Original issue reported on code.google.com by
jkgren...@gmail.com
on 10 Feb 2015 at 4:22