search

bioinform / rnacocktail

Other
86 stars 48 forks source link

Keep moving #16

Open chunjie-sam-liu opened 5 years ago

chunjie-sam-liu commented 5 years ago

RNAcocktail is a very impressive tool to process almost all kinds of analyses based on RNA-seq data. But the tools integrated in the RNAcocktail has not been updated for a long time. can you upgrade tools in RNAcocktail, for example salmon. And RNA splicing is also a major part of analyzing RNA-seq data, DART, SpliceAI improve splicing prediction.

msahraeian commented 4 years ago

@chunjie-sam-liu I have upgraded tools to latest version at #17 (for now I upgraded salmon to 0.11.0 since that is the latest version that supports SMEM option). The new docker image (v0.3.0) have these tools pre-installed.

droeatumn commented 4 years ago

Thank you. Would you mind upgrading HISAT2 as well?

msahraeian commented 4 years ago

The new release docker already has the latest HISAT2(v2.1.0).

msahraeian commented 4 years ago

I upgraded salmon to 0.11.0 since that is the latest version that supports SMEM option. Based on our analysis, we found salmon to perform better in SMEM mode.

On Thu, Nov 28, 2019 at 7:58 AM droeatumn notifications@github.com wrote:

My mistake. How about salmon? I see 0.11.0 in the docker image, but the latest is 1.0.0. Is that right?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bioinform/rnacocktail/issues/16?email_source=notifications&email_token=ACUU4YCV4B4MQSUKJ4YI253QV7TBFA5CNFSM4HOKXV32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFM7OJQ#issuecomment-559544102, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACUU4YF2VGGBVWNDZIM42LDQV7TBFANCNFSM4HOKXV3Q .