Forum: Bioinformatics
03-26-2015, 09:47 AM
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Replies: 28
Views: 61,001
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Forum: Bioinformatics
09-18-2012, 12:15 AM
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Replies: 8
Views: 11,932
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Forum: Bioinformatics
07-06-2012, 01:50 AM
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Replies: 1
Views: 1,140
when does BWA writes the outpu .sai
This might be a dumb question, but I can't find the answer anywhere and also don't have to possibility to test it right now.
When does BWA wrirte the output to the *.sai file?
Is it happening on...
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Forum: De novo discovery
09-19-2011, 06:50 AM
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Replies: 8
Views: 12,698
I am working with illumina reads (PE 100bp).
...
I am working with illumina reads (PE 100bp).
well the minimum kmer coverage is default 1 for trinity for oases it is 3, so maybe results will be better with trinity. but of course a lot depends on...
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Forum: De novo discovery
09-15-2011, 01:47 AM
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Replies: 8
Views: 12,698
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Forum: De novo discovery
06-28-2011, 03:11 AM
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Replies: 58
Views: 51,849
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Forum: Bioinformatics
05-21-2011, 02:44 AM
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Replies: 31
Views: 10,110
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Forum: Bioinformatics
05-20-2011, 10:27 AM
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Replies: 31
Views: 10,110
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Forum: De novo discovery
05-11-2011, 06:13 AM
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Replies: 58
Views: 51,849
on the oases malinglist Daniel Zerbino wrote: ...
on the oases malinglist Daniel Zerbino wrote:
"Are you compiling Oases with the OPENMP flag? This indeed is not allowed
by the Oases Makefile, as Oases will not be accelerated by the parallel ...
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Forum: De novo discovery
05-04-2011, 11:19 AM
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Replies: 16
Views: 6,999
yes, it is the first hit when you google...
yes, it is the first hit when you google "definition: N50"
separate to "shortpaired" I assume. So you can use 2 different PE libraries with different insert sizes, but maybe I am wrong.
Total...
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Forum: Bioinformatics
05-04-2011, 03:48 AM
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Replies: 2
Views: 1,384
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Forum: RNA Sequencing
05-04-2011, 02:48 AM
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Replies: 12
Views: 4,000
no, i don't think that the non-normalisation is...
no, i don't think that the non-normalisation is the reason here, but keep in mind that you coverage is not consistent over all transcripts. So it might get some transcripts better assembled with a...
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Forum: RNA Sequencing
05-04-2011, 01:54 AM
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Replies: 12
Views: 4,000
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Forum: De novo discovery
05-04-2011, 01:47 AM
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Replies: 16
Views: 6,999
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Forum: De novo discovery
05-02-2011, 09:21 AM
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Replies: 8
Views: 5,182
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Forum: Bioinformatics
05-02-2011, 09:15 AM
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Replies: 10
Views: 5,145
so why not trim the reads first and then try to...
so why not trim the reads first and then try to map without quality values? You don't want to assemble bad reads anyway and they mostly won't overlap if you don't trim. Or you could just cut all your...
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Forum: Bioinformatics
05-02-2011, 02:08 AM
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Replies: 10
Views: 5,145
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Forum: Bioinformatics
05-02-2011, 01:19 AM
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Replies: 10
Views: 5,145
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Forum: De novo discovery
05-02-2011, 01:17 AM
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Replies: 8
Views: 5,182
so you have references of your genes you are...
so you have references of your genes you are looking for and what %-identity you expect in the sequence? Blasting all your reads against your reference genes seems not to be the smartest way. ;-)...
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Forum: De novo discovery
04-28-2011, 03:58 AM
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Replies: 16
Views: 6,999
i have no clue what genegenious is and on what...
i have no clue what genegenious is and on what algorithm it is based. So if it is a ovelap-based method, yes it is possible and depends on kmer, amount of reads you have, expected coverage, read...
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Forum: De novo discovery
04-28-2011, 12:17 AM
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Replies: 16
Views: 6,999
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Forum: De novo discovery
04-26-2011, 08:25 AM
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Replies: 16
Views: 6,999
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Forum: De novo discovery
04-26-2011, 02:17 AM
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Replies: 16
Views: 6,999
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Forum: De novo discovery
04-20-2011, 08:50 AM
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Replies: 58
Views: 51,849
depending on your number of reads it takes...
depending on your number of reads it takes "hours" till it finishes.
5hours
30GB RAM
with around 70.000.0000 reads with average length 90
you can speed things up with the new parallel mode...
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Forum: RNA Sequencing
04-20-2011, 01:17 AM
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Replies: 12
Views: 4,000
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