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Old 11-19-2013, 11:44 AM   #1
Sergio.pv
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Default min length and max length with fastx tookit

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!
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File Type: pdf FASTQ-tools-ion-torrent.pdf (395.9 KB, 12 views)

Last edited by Sergio.pv; 11-19-2013 at 12:48 PM.
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Old 11-19-2013, 12:19 PM   #2
lindenb
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cross posted on biostars: http://www.biostars.org/p/86850/
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Old 11-19-2013, 12:25 PM   #3
Sergio.pv
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Yes, that was I.
I am really stuck with this problem, so i postd it in both sites.

Best!
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Old 11-19-2013, 12:38 PM   #4
GenoMax
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Curious as to why you need to limit the maximum length?
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Old 11-19-2013, 12:47 PM   #5
Sergio.pv
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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.
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Old 11-19-2013, 01:33 PM   #6
dpryan
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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).
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Old 11-19-2013, 01:53 PM   #7
Sergio.pv
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yes you are right.
My attempt is to analize data from the <200 nt RNA fraction, to find the most expressed miRNA candidates.

Best!
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