Is there any way to exclude the read lengths below certain length say 100bp for denovo assembly using Velvet
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Originally posted by nxtgenkid10 View PostIs there any way to exclude the read lengths below certain length say 100bp for denovo assembly using Velvet
Out of curiosity, why are you wanting to do this? If your data is 454 then Newbler will probably do a better job, in my experience, and if your data is from an Illumina 100bp library then you are not really going to have any variation in read length.
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Originally posted by SES View PostI don't think there is a way to specify the reads that go into the contigs with velvet (like you can with Newbler). You can specify the minimum contig length in Velvet, but that is not exactly what you wanted. The best thing to do would be to filter the reads before assembly.
Out of curiosity, why are you wanting to do this? If your data is 454 then Newbler will probably do a better job, in my experience, and if your data is from an Illumina 100bp library then you are not really going to have any variation in read length.
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Originally posted by nangillala View PostSo why don't you trust your reads below 100 bp? (Maybe there's a reason for this).
Velvet uses k-mers, so the reads will be "splitted" into shorter fragments anyways.
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Originally posted by nxtgenkid10 View PostThe thing is that I'm lokking for the reads with Q30+ and feels it may have some adapter contamination; aS i told before I'm new to this and looking for options in the tools to make an clear interpretation from the data in hand
I'm not sure what kind of reads you have: Illumina? 454? SFF format? Fastq?
Assuming you have files in fastq format you could use the fastx toolkit
to get rid of adapters (Fastq_Clipper). You can also use it to discard sequences shorter than a threshold you choose.
You may also like the Fastq Quality Filter. You can choose the minimum quality score to keep and the minimum percent of bases that must have this quality.
Hope that helps!?
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Originally posted by nangillala View PostHi,
I'm not sure what kind of reads you have: Illumina? 454? SFF format? Fastq?
Assuming you have files in fastq format you could use the fastx toolkit
to get rid of adapters (Fastq_Clipper). You can also use it to discard sequences shorter than a threshold you choose.
You may also like the Fastq Quality Filter. You can choose the minimum quality score to keep and the minimum percent of bases that must have this quality.
Hope that helps!?
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