Setting up a portable RNA-Seq pipeline for CBIO

05/17/2018

02:54 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Katie I've renamed the repos to https://github.com/uct-cbio/RNAseq-pipeline . In your Git config you just need to mod... Gerrit Botha

04/25/2018

12:57 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Thanks Gerrit,
Will go through the results and see at which steps we might want to adjust parameters. Yes it's fin... Katie Lennard

11:55 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

HI Katie,
This is good news, thanks for testing a complete run from beginning to end.
Also , thanks for openin... Gerrit Botha

10:51 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

Test run completed successfully! Input and output at /researchdata/fhgfs/katie/NGI-RNAseq-test/ (permissions open to ... Katie Lennard

04/24/2018

03:18 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Andrew has enabled sendmail to send emails from the compute nodes. I tested
~~~
gerrit@srvslshpc602:~> echo "Subj... Gerrit Botha

04/23/2018

05:46 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

The run completed successfully.
Here was the rest of the screen logs.
~~~
....
[50/552125] NOTE: Process `m... Gerrit Botha

01:03 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

OK the MarkDuplicates process ran out of memory. I added a section here: https://github.com/uct-cbio/RNAseq/commit/71... Gerrit Botha

11:42 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

STAR alignment on sample38 and 39 completed successfully. It now however failed on running Picard MarkDuplicates. Can... Gerrit Botha