min length and max length with fastx tookit

[Sergio.pv]

Hello everyone,
i was wondering if there's a way to filter fastq reads based on minimun and maximun length. Plus trimming at minimun quality value.

this is the closest i've came out with:

fastq_quality_trimmer -v -t 20 -l 16 -i myfile.fastq -o myfile.trimmed -Q 33

however, no option to choose the maximun length appears to exists. Is it possible that there are hidden commands that i don't know about (such as -Q 33). According to a technical note from ion torrent, there is an option to limit the maximimun length and it's contained in fastq_quality_trimmer.

I would greatly appretiate the help,
Best regards!

[lindenb]

cross posted on biostars: http://www.biostars.org/p/86850/

[Sergio.pv]

Yes, that was I.
I am really stuck with this problem, so i postd it in both sites.

Best!

[GenoMax]

Curious as to why you need to limit the maximum length?

[Sergio.pv]

As suggested by the ion torrent's technical note, this would leave little or no adapter sequence in the reads.
I have attached the mentioned note.

[dpryan]

It's usually good to mention in this context that you're looking at miRNAs or other short RNAs. At least I assume that's what you're doing since this is specifically mentioned only for miRNA-seq. I (and likely others) would argue that simply quality and adapter trimming should still suffice (just decrease the overlap threshold for the adapter sequence if you want to be more conservative).

[Sergio.pv]

yes you are right.
My attempt is to analize data from the <200 nt RNA fraction, to find the most expressed miRNA candidates.

Best!