Max Length With Fastx Tookit

Question

[serpalma.v]

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!

[Pierre Lindenbaum]

cross posted on SE: http://seqanswers.com/forums/showthread.php?t=35983

[serpalma.v]

is that a bad thing, sorry I am not familiar with forum's rules and regulations. Best

[Devon Ryan]

Those of us on both sites kind of hate it. Inevitably, a question will get answered on both sites, which just means that someone wasted their time.

[serpalma.v]

Can be, however that's not everybody. And based on this post, i've gotten different feedback from both sources.

Answer 1

[Istvan Albert]

cutadapt and many other tools can filter for maximum lenght

  -m LENGTH, --minimum-length=LENGTH
                        Discard trimmed reads that are shorter than LENGTH.
                        Reads that are too short even before adapter removal
                        are also discarded. In colorspace, an initial primer
                        is not counted (default: 0).
    -M LENGTH, --maximum-length=LENGTH
                        Discard trimmed reads that are longer than LENGTH.
                        Reads that are too long even before adapter removal
                        are also discarded. In colorspace, an initial primer
                        is not counted (default: no limit).