User: vincent.lacroix

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1 year, 3 months ago
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v**************@univ-lyon1.fr

Posts by vincent.lacroix

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Help to interpret results of kisSplice
... Dear user, The introductory slides we use in our trainings should help you. You can find them here: http://kissplice.prabi.fr/training/ Best regards, Vincent ...
written 3 days ago by vincent.lacroix50
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Answer: A: Variant detection in RNA seq datasets without a reference using kISSPLICE.
... Dear Koushik Ponnanna, Thanks for your interest in KisSplice. Below are some answers to your questions: 1- When you load the reads from a pair separately, C1 will correspond to the read count of read 1, and C2 will correspond to the read count of read 2. In principle, C1+C2 should give you the read ...
written 3 days ago by vincent.lacroix50
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Answer: A: KisSplice output for SNPs type 0a - for are the identifiers Q1_.. Q2_.. Qn_..
... Dear user, I am sorry for the slow reply. Indeed, the user guide does not explain this point. We should include this in the next version. Q1_.. Q2_.. Q3_.. Q4_.. correspond to the average quality of the bases covering the SNP in your data. If the average quality is low, then it is likely that your ...
written 3 days ago by vincent.lacroix50
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Answer: A: Incorrect codon sequences reported in kissplice2reftranscriptome output?
... Dear Andres, Thanks for sending the files. It seems that the problem comes from the fact that you used a different kmer value in KisSplice and KisSplice2RefTranscriptome. We are not catching this error correctly in kissplice2reftranscriptome and it was indeed not obvious to know what the problem was ...
written 4 months ago by vincent.lacroix50
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Answer: A: Incorrect codon sequences reported in kissplice2reftranscriptome output?
... Dear Andres, Columns Codon 1 and Codon 2 should be distinct, otherwise there would be no SNP. Could you send me a sample of your data so that we try to reproduce your bug ? You can send directly at vincent dot lacroix at univ-lyon1 dot fr Thanks ! Vincent ...
written 4 months ago by vincent.lacroix50
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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 5 months ago by vincent.lacroix50
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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 5 months ago by vincent.lacroix50
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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 6 months ago by vincent.lacroix50
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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 7 months ago by vincent.lacroix50
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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 7 months ago by vincent.lacroix50

Latest awards to vincent.lacroix

Scholar 13 months ago, created an answer that has been accepted. For A: Error in running "diffExpressedVariants" function in kissDE R package

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