[mira_talk] Re: Difference between singlets and NO_OVERLAP in debris
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 17 Mar 2016 22:47:56 -0400
On 17 Mar 2016, at 1:36 , wakamoto5959@xxxxxxxxxxx wrote:
I have a question about the difference between singlets and NO_OVERLAP
sequences in debrislist file.
Singlets are important for my study. So I set sssip=yes and mrpc=1.
I see from the manifest you are doing RNASeq. Please be very, very, very … very
careful when interpreting “singlets”. To put it very bluntly: if you are basing
research on rare single sequences, you are doing it wrong. Yes, I know, rare
transcripts and all that. But there are also chimeras, PCR artefacts and other
sequencing related “unique” transcripts which are simply trash. And I fear that
these outweigh “real” rare transcripts if not doing ultra-high-depth sequencing.
So I get “contigs” with single read. I really appreciate this function.
However, I also realised many sequences are in debrislist with NO_OVERLAP
annotated.
Those NO_OVERLAP sequences in debrislist file are long and looking very good
sequences.
How those sequences in debrislist file with NO_OVRELAP annotatation are
different from singlets?
NO_OVERLAP means: MIRA did not find any other reads with which to overlap these
sequences. Yes, these could have been written out as singlets, but as my
experience with them has been such that I believe that 99.x% of these are
simply real junk, MIRA doesn’t bother with them and puts them into debris. If
you really, really, really want them, use the debris file to create a file of
readnames which will allow to get them out of the readpool.maf file of mira:
grep NO_OVERLAP debris.txt | cut -f 1 >snames.txt
miraconvert -n snames.txt -C readpool.maf mysinglets.fasta
“Normal” singlets did show some overlap to other reads at one point or another,
and therefore will get written out to result files.
B.
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