[mira_talk] Re: MIRA 3.2.1 VERSION MiraSearchESTSNPs not working
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 13 Feb 2011 14:38:41 +0100
On Sunday 13 February 2011 14:21:31 walter kiprotich wrote:
> I am experiencing problems with assembling and SNPs search (ver:
> mira_3.2.1_linux-gnu_x86_64) I use miraSearchESTSNPs pipeline to assemble
> 454 reads, but the step3_info_snplist.txt file does not contain any SNPs
> even though i can find in log file for example: ... Found
> - 0 new Strong RMB (SRMc)
> - 0 new Weak RMB (WRMc)
> - 244 SNP
> positions tagged.Transfering reads to readpool.
> Done...................
> Saving SNP list to file: step3_d_info/step3_info_snplist.txt What is the
> problem with my miraSearchESTSNPs pipeline. All my input files are okey
> and steps 1&2 are perfect with all files having results walter kosgei
The snplist file is for other uses: when mapping or assembling with data which
has GenBank annotation attached. Your data obviously has not.
However, what you are searching for is in the
step3_d_info/step3_info_consensustaglist.txt
file. Search for SROc, SAOc and SIOc tags. MCVc might also apply if not at the
start or end of a contig.
B.
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