Thank you very much! Very helpful. I understand now.
Yi
2015-08-15 19:05 GMT+08:00 Bastien Chevreux <bach@xxxxxxxxxxxx>:
On 15 Aug 2015, at 4:28 , Huang Yi <huang.y.hy@xxxxxxxxx> wrote:
[…]
MIRA ran four minutes only then quit. The last several lines of log are:
[…]
MIRA did not quit, it would have written a good-bye message (if everything
went fine) or an error message (if it encountered a problem). No message
means: the process must have been killed by the OS. Probably because of
memory errors.
[…]
Is 994 coverage too high?
Way too high. Target a coverage of ~70-80x
If so, would you please tell me how to reduce the coverage
If you Google for “reduce Illumina coverage” or “subsample illumina reads”
you will find tons of ways to do that. Personally, I simply use the Unix
“head” command: simple, effective, and no one has been able to prove that
random subsampling performs better. Though with the kind of coverage you
have, one might really start to find such scenarios. In that case, I think
seqtk might be useful.
B.
PS: and next time you go into sequencing, talk to your provider about “I
just need 100x coverage, what can you propose?” … that could save you some
money
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