update to Salmon 0.14 - Githubissues

hms-dbmi / dseqr

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

https://docs.dseqr.com

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update to Salmon 0.14 #77

Closed alexvpickering closed 5 years ago

alexvpickering commented 5 years ago

Changes in Salmon release 0.14 are based on following paper: Alignment and mapping methodology influence transcript abundance estimation.

To do:

[x] update README
[x] rebuild gencode index with decoy sequences (for scRNA-seq)
[x] update read_scseq for new alevin output format
[ ] rebuild ensdb index with decoy sequences (for bulk RNA-seq)
[ ] re-run example SJIA analyses
[ ] re-run example IBD analysis

Note: using develop branch of salmon because of https://github.com/COMBINE-lab/salmon/issues/379 and https://github.com/COMBINE-lab/salmon/issues/380

alexvpickering commented 5 years ago

Closed in favor of kallisto #79