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LuyiTian / scPipe

a pipeline for single cell RNA-seq data analysis
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Fixes #117 #119

Closed Shians closed 5 years ago

Shians commented 5 years ago

This pull request addresses #117 and #116. With the manual removal of the unreasonably long entries, the GFF becomes parsable, but scPipe could not process the Dbxref column correctly because "GeneID" is usually the first element. After the changes the GFF will be processed, but GeneIDs could not be found in some exons and a message is produced: NA found in GeneID of 222 of 324663 entries, automatically removing these entries.

audreystott commented 5 years ago

Thanks Shian for updating the code. Is it ready for re-installation on R?

Shians commented 5 years ago

@audreystott You will have to install it through devtools::install_github("LuyiTian/scPipe"), it won't be properly updated on Bioconductor until the next release cycle.

PeteHaitch commented 5 years ago

@shians if it's a bug fix rather than a new feature it can and probably should be ported to the release

audreystott commented 5 years ago

Ok that's how I installed mine previously so that's great. Thank you!