Thanks Devon,
I think now I got it ;-). We are running 17.05 I might not have the
"Summary Options" ? I cannot find them...
But maybe I can use the flagstat tool for now.
Cheers Jochen
On 02.05.2018 16:34, Devon Ryan wrote:
By default the logs are just to stdout. You need to use one of the
options (under "Summary Options" on the version on our instance) if
you want things saved as a history item.
Devon
--
Devon Ryan, Ph.D.
Email: [email protected]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <[email protected]> wrote:
That's also an interesting tool. Which gives almost the same result as in
the log file of at HISAT output. I'm not sure why the number of mapped reads
are not 100% identical...
but anyway can someone tell me, or maybe Devon did already, where is the log
info of HISAT saved?
Cheers Jochen
On 02.05.2018 12:37, Langhorst, Brad wrote:
Flagstat might be a good choice here…
Brad
On May 2, 2018, at 1:48 AM, Jochen Bick <[email protected]> wrote:
Hi Devon,
do you mean Alignment Summary? How can I access that information and use
it for an other tool.
Cheers Jochen
On 26.04.2018 14:14, Devon Ryan wrote:
There are two alignment summary options in the wrapper that will cause
most/all of that to be written to a history item. They're under
"Summary Options".
Devon
--
Devon Ryan, Ph.D.
Email: [email protected]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[email protected]>
wrote:
Hi,
I would like to use the info (log) HISAT is showing, for another tool.
e.g.:
26781724 reads; of these:
26781724 (100.00%) were unpaired; of these:
2445411 (9.13%) aligned 0 times
20399099 (76.17%) aligned exactly 1 time
3937214 (14.70%) aligned >1 times
90.87% overall alignment rate
[bam_sort_core] merging from 21 f
Is it possible to access these logs?
Cheers Jochen
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