[mira_talk] Re: Is quality file necessary for assembly after qual filtering
- From: "Raj Kumar, Praveen Kumar" <rajkump@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 22 May 2013 15:09:46 -0400
Thank you very much
On Wed, May 22, 2013 at 2:53 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On May 22, 2013, at 17:26 , "Raj Kumar, Praveen Kumar" <
> rajkump@xxxxxxxxxxx> wrote:
> > I kind of have a general question regarding de-novo assembly. I am
> using both Prinseq (for qual filtering) and Seqclean (adapter trimming +
> trim polyA tail + etc) for cleaning my cDNA sequences.
>
> Ummm … yes, you can use these tools. Or use the multitude of clipping
> routines in MIRA.
>
> Your choice.
>
> > Seqclean works only with fasta files.....so I end up with fasta
> sequences without qual (quality) scores. Is it OK to use only fasta seqs
> for assembly and anyhow I did qual filtering already?
>
> No. No, no, no … and no.
>
> > OR Is the qual scores used for anyother purpose in assembly other than
> qual filtering?
>
> Yes.
>
> > In other words what are the uses of qual scores in assembly other than
> qual filtering?
>
>
> http://mira-assembler.sourceforge.net/docs-dev/DefinitiveGuideToMIRA.html#sect_ref_never_without_quality_values
>
> I hope I was clear enough :-)
>
> B.
>
>
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--
Praveen K. Raj Kumar,
Ph.D Candidate,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210
http://www.users.muohio.edu/rajkump/index.html
http://conifergdb.muohio.edu/bioinfolab6p1/tiki-index.php?page=Praveen+K.+Raj+Kumar
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