User: vincent.lacroix

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Posts by vincent.lacroix

<prev • 8 results • page 1 of 1 • next >
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Answer: A: The installation of KissDE
... Dear Tom, We just posted a new version of KissDE here: http://kissplice.prabi.fr/tools/kissDE/ KissDE 1.5.0 has been tested on R-3.4.0, and on our system, we did not experience any trouble with dependencies. Best, Vincent ...
written 10 days ago by vincent.lacroix30
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Answer: A: The installation of KissDE
... Dear Tom, KissDE has been tested on R-3.3.3, where the version of DSS is 2.14.0 It seems that version 2.16.0 of DSS has a new dependency (DelayArray), which is causing you trouble. A way around this could be to use version 2.14.0 of DSS. Can you try this ? Best, Vincent ...
written 10 days ago by vincent.lacroix30
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Answer: A: KisSplice2refgenome error message
... Dear Sophie, I think the best solution is to use k2rg without any option. kissplice2refgenome -a annotation_file.gtf output_starlong.sam This should work fine. The other options are used to have a good estimation of the Percent Spliced In (PSI). If you do not use them, the output file should ...
written 5 weeks ago by vincent.lacroix30
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Answer: A: Error in running kissplice2reftranscriptome
... Dear Chiara and k2rt users, I apologise for my slow response on this forum. I had posted this message on the kissplice-users list, but I had forgotten to answer also on the forum. A new version of k2rt which solves this bug is now available here; http://kissplice.prabi.fr/tools/kiss2rt/ Thanks for ...
written 12 weeks ago by vincent.lacroix30
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Answer: A: gmap psl parsing in kissplice2refgenome
... Dear Fabrice, In principle, kissplice2refgenome takes both .psl and .sam as input. But in practice, we mostly use .sam files produced by STAR, using .gtf files dowloaded from Ensembl. A typical workflow is given here: http://kissplice.prabi.fr/pipeline_ks_farline/ Overall we recommand to use STAR ...
written 12 weeks ago by vincent.lacroix30
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Answer: A: how to signify experiments/replica files in kissplice
... Dear Celine, If you have 2 conditions and 2 replicates, which correspond to 4 fastq files, say c1r1.fq, c1r2.fq, c2r1.fq, c2r2.fq, then you can run kissplice with the following command kissplice -r c1r1.fq -r c1r2.fq -r c2r1.fq -r c2r2.fq ...
written 5 months ago by vincent.lacroix30
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Answer: A: Error in running "diffExpressedVariants" function in kissDE R package
... Dear all, This bug is now solved. It was related to KissDE's dependency to Biobase and DSS. These packages had been upgraded, and there were compatibiliy issues to fix. The estimation of the dispersion is now also better. Hence, the final output of KissDE 1.4.0 is expected to change compared to ...
written 5 months ago by vincent.lacroix30
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Answer: A: Error in running "diffExpressedVariants" function in kissDE R package
... Dear c.evang, KissDE requires replicates. This is most likely the cause of your problem. I undertand you have two biological conditions (mDr, and WW). If you have replicates for each condition, then you need to run KisSplice on all replicates of all conditions. Those are 4 reads files (or possibly ...
written 8 months ago by vincent.lacroix30

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Scholar 8 months ago, created an answer that has been accepted. For A: Error in running "diffExpressedVariants" function in kissDE R package

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