User: vincent.lacroix

Reputation:
40
Status:
New User
Location:
Last seen:
2 months, 2 weeks ago
Joined:
1 year, 1 month ago
Email:
v**************@univ-lyon1.fr

Posts by vincent.lacroix

<prev • 10 results • page 1 of 1 • next >
1
vote
2
answers
177
views
2
answers
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 11 weeks ago by vincent.lacroix40
0
votes
2
answers
177
views
2
answers
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 11 weeks ago by vincent.lacroix40
0
votes
2
answers
226
views
2
answers
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 3 months ago by vincent.lacroix40
1
vote
2
answers
226
views
2
answers
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 3 months ago by vincent.lacroix40
0
votes
1
answer
158
views
1
answers
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 4 months ago by vincent.lacroix40
1
vote
2
answers
403
views
2
answers
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 5 months ago by vincent.lacroix40
0
votes
1
answer
176
views
1
answers
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 5 months ago by vincent.lacroix40
0
votes
3
answers
314
views
3
answers
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 8 months ago by vincent.lacroix40
0
votes
2
answers
552
views
2
answers
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 8 months ago by vincent.lacroix40
1
vote
2
answers
552
views
2
answers
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 11 months ago by vincent.lacroix40

Latest awards to vincent.lacroix

Scholar 11 months ago, created an answer that has been accepted. For A: Error in running "diffExpressedVariants" function in kissDE R package

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 487 users visited in the last hour