Velevt Controll Read Length

[nxtgenkid10]

Hi,
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!?

454 Fastq and thanks that is really helpful

[nangillala]

The 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

Hi,
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!?

[nxtgenkid10]

So 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.

The 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

[nangillala]

So 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.

[nxtgenkid10]

I 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.

yes i agree with you i have data with newbler am trying out the results with other assemblers too and see the differences; as i'm new to this arena wanna to know how these tools work .. and thank you for responding back

[SES]

Is there any way to exclude the read lengths below certain length say 100bp for denovo assembly using Velvet

I 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.

[nxtgenkid10]

Is there any way to exclude the read lengths below certain length say 100bp for denovo assembly using Velvet