[mira_talk] Re: force MIRA to produce only singletons and no debris

On Monday 21 February 2011 11:02:52 Yvan Wenger wrote:
>  [...]
> I am satisfied with the assembly itself, but performing a blast tells
> me that 1437 sanger reads I inputed do not have any counterpart in the
> cleaned_out.unpadded.fasta file... how can that be? On what basis are
> these sequences discarded? I will end up fetching all those sanger
> input that do not have a hit in the final fasta file produced, but I
> am still curious.

Hmmm ... at first sight I'd say that from the command line, everything looks 
right.

BTW, you do not need BLASt to see whether a read has made it into the 
assembly: the debris file or the contigreadlist file (both in the info 
directory) should give you the same information.

Back to your problem: please have a look at the clipping log file (in the log 
directory) and search there for hints whether clipping kille your reads.

If there are still problems remaining, you can make me available the (reduced) 
data set and I'll have a look.

B.

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