[mira_talk] Re: medium error: Very High Average Coverage
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 30 May 2015 16:23:38 +0200
On 30 May 2015, at 6:58 , Rameez Mj <rameez03online@xxxxxxxxx> wrote:
Dear fernandez, I filtered my fastq using PRINSEQ. Removed all kinds of
duplicates and trimmed off the reads to maximum 210bp. only 2.81% of my data
is removed and now average coverage came down to 120x from 129x. Is there any
option in PRINSEQ to randomly eliminate or extract a specified percentage of
reads from the large fast file?
Instead of trying to jump through all sorts of interesting hoops, I suggest the
following:
head -XXXXX input.fastq >reduced.fastq
Replace “XXXXX” by any number you wish (preferably calculated from the coverage
numbers you got) and make sure that number is divisible by 4 :-)
B.
PS: yes, it’s crude.
PPS: you might be interested in following this helpful advice from the MIRA
manual:
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_pd_illumina
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