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11-19-2013, 11:44 AM
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#1 |
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Member
Location: Berlin Join Date: Jul 2013
Posts: 20
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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! Last edited by Sergio.pv; 11-19-2013 at 12:48 PM. |
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11-19-2013, 12:19 PM
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#2 |
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Senior Member
Location: France Join Date: Apr 2010
Posts: 143
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cross posted on biostars: http://www.biostars.org/p/86850/
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11-19-2013, 12:25 PM
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#3 |
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Member
Location: Berlin Join Date: Jul 2013
Posts: 20
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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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11-19-2013, 12:38 PM
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#4 |
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Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,080
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Curious as to why you need to limit the maximum length?
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11-19-2013, 12:47 PM
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#5 |
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Member
Location: Berlin Join Date: Jul 2013
Posts: 20
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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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11-19-2013, 01:33 PM
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#6 |
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Devon Ryan
Location: Freiburg, Germany Join Date: Jul 2011
Posts: 3,480
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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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11-19-2013, 01:53 PM
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#7 |
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Member
Location: Berlin Join Date: Jul 2013
Posts: 20
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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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