rnaseq-pipeline

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RSEM temporary file cleanup does not always work

1

I think it might relate to NFS.

arteymix

Currently, we use the SRA format for FASTQ headers which prefix the SRR run accession to the original string from the sequencer. This format is not compatible with ArrayExpress and...

arteymix

In the current setup, it's possible that the AlignSample task get scheduled on a different node than the matching DownloadSample task which disrupt the NFS caching. We could first start...

arteymix

Make it less disruptive to queue new experiments

1

arteymix

This would basically resolve #13 since we would pull the information from SRA/GEO/Gemma instead of requesting it. For the local source, we would still need a flag to override a...

arteymix

arteymix

[RSeQC](http://rseqc.sourceforge.net/) provide a wide range of tools for that purpose.

arteymix

arteymix

Handle SRA experiments with multiple lanes mapped on distinct runs

1

- [ ] check the runinfo to make sure the sample can be combined (i.e. same pairedness, insert size, read length) - [ ] make sure we don't process the...

arteymix

- [ ] detect platforms/datasets that are suitable for Cell Ranger - [ ] add a task for generating the reference (optional, we can use those provided by Cell Ranger)...

arteymix