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Published 20 hours ago • verified publisher icon bioinform

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Open chunjie-sam-liu opened this issue 5 years ago • 4 comments

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.

chunjie-sam-liu avatar May 21 '19 13:05 chunjie-sam-liu

@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.

msahraeian avatar Nov 15 '19 23:11 msahraeian

Thank you. Would you mind upgrading HISAT2 as well?

droeatumn avatar Nov 22 '19 01:11 droeatumn

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

msahraeian avatar Nov 22 '19 04:11 msahraeian

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 [email protected] 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?

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msahraeian avatar Nov 28 '19 23:11 msahraeian