User: vincent.lacroix

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Posts by vincent.lacroix

<prev • 16 results • page 1 of 2 • next >
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Answer: A: k2rt couldn't deal with type3(indel) fasta?
... Dear User, Unfortunately, k2rt does not support indels for now. This is something we are interested in developing, but we have nothing ready. Best regards, Vincent ...
written 10 hours ago by vincent.lacroix70
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Answer: A: Calling de novo SNPs between two species with KisSplice
... Dear user, The running time depends on the number of SNPs you have. KissDE should take ~2h for 50000 SNPs. It seems you have many more SNPs. If most of them are cases where one allele got fixed in one species and the other allele got fixed in the other species, then running KissDE might be an ove ...
written 7 weeks ago by vincent.lacroix70
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Answer: A: Calling de novo SNPs between two species with KisSplice
... Dear user, Finding divergent sites between two species is what we did for D. mojavensis and D. arizonae in our paper. Like you, we had two paired-end samples for each species. I think that KissDE fits your needs. Below is an example of the KisSplice output we obtain: \>bcc_9|Cycle_0|Type_0a|uppe ...
written 8 weeks ago by vincent.lacroix70
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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 months ago by vincent.lacroix70
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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 months ago by vincent.lacroix70
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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 months ago by vincent.lacroix70
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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 7 months ago by vincent.lacroix70
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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 7 months ago by vincent.lacroix70
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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 8 months ago by vincent.lacroix70
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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 8 months ago by vincent.lacroix70

Latest awards to vincent.lacroix

Scholar 16 months ago, created an answer that has been accepted. For A: Error in running "diffExpressedVariants" function in kissDE R package

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