search

RabadanLab / arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq
GNU General Public License v3.0
114 stars 49 forks source link

determination of single-end vs paired-end data #46

Closed alexvpickering closed 3 years ago

alexvpickering commented 3 years ago

Note that default behaviour changed with #44 (breaking change).

Old behaviour: set as single-end if one fastq file supplied, paired-end if two supplied. Change with #44: default is paired-end unless --single flag present. Rationale: can be two fastq.gz files for single-end and e.g. 4 for paired-end (see kallisto manual)

Let me know if you would like to change it back to the old behaviour. It got added to #44 by mistake when I was updating it to reflect my own preference.

IoanFilip2 commented 3 years ago

Thanks, I think it works as is, with the latest update (#44). May need to update the README.

Ioan

On Mon, Sep 28, 2020 at 6:27 PM Alex Pickering notifications@github.com wrote:

Note that default behaviour changed with #44 https://github.com/RabadanLab/arcasHLA/pull/44 (breaking change).

Old behaviour: set as single-end if one fastq file supplied, paired-end if two supplied. Change with #44 https://github.com/RabadanLab/arcasHLA/pull/44: default is paired-end unless --single flag present. Rationale: can be two fastq.gz files for single-end and e.g. 4 for paired-end (see kallisto manual https://pachterlab.github.io/kallisto/manual)

Let me know if you would like to change it back to the old behaviour. It got added to #44 https://github.com/RabadanLab/arcasHLA/pull/44 by mistake when I was updating it to reflect my own preference.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/RabadanLab/arcasHLA/issues/46, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACT54QDI6O7WHLFBFGNUCH3SIEEVZANCNFSM4R5BIDEQ .