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 >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/ > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
