User: vincent.lacroix

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Posts by vincent.lacroix

<prev • 19 results • page 1 of 2 • next >
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Answer: A: kissDE diffExpressedVariants Error in nls
... Dear Ovidiu, We double checked on several datasets and using the cheap guessing of the nls function indeed works well as it does not affect the final results. We will likely update the code accordingly in the next release of kissDE. Thanks for pointing this out. In the meantime, other users confro ...
written 3 months ago by vincent.lacroix80 • updated 5 weeks ago by genomax57k
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Answer: A: kissplice2reftranscriptome interpreting output
... Hi Vanessa, I am not sure I understand your question. The column SNP_position of the main output file of k2rt should give you the position of the SNP in the reference. The only tricky thing to remember is that this coordinate is 0-based. If you simply need the position of the SNP in the reference, ...
written 7 months ago by vincent.lacroix80
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Answer: A: kissplice2reftranscriptome interpreting output
... Hi Lucaciu, All the formats we use in our pipeline (.bed, .psl) are 0-based, hence the SNP position we output in the final table is also 0-based. If you want to use samtools faidx (which is 1-based), you should type : samtools faidx 02_Trinity.fasta TRINITY_DN9185_c0_g2_i1:201-205 You will ob ...
written 8 months ago by vincent.lacroix80
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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 9 months ago by vincent.lacroix80
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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 10 months ago by vincent.lacroix80
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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 10 months ago by vincent.lacroix80
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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 12 months ago by vincent.lacroix80
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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 12 months ago by vincent.lacroix80
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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 12 months ago by vincent.lacroix80
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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 16 months ago by vincent.lacroix80

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Scholar 2.1 years ago, created an answer that has been accepted. For A: Error in running "diffExpressedVariants" function in kissDE R package

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