User: vincent.lacroix

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Posts by vincent.lacroix

<prev • 23 results • page 1 of 3 • next >
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Answer: A: Problem with ks_debruijn4 on large dataset in KisSplice
... Dear David and all, KisSplice v2.5.0 is now available for all users and can be downloaded here: http://kissplice.prabi.fr It indeed is much faster for graph construction thanks to the integration of bcalm (https://github.com/GATB/bcalm). For large datasets, we advise users to increase the value of ...
written 6 months ago by vincent.lacroix130
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Answer: A: Problem with ks_debruijn4 on large dataset in KisSplice
... Dear David, Apologies for the slow reply, I will try to answer your questions. Indeed KisSplice 2.4.0 does not scale well to very large datasets. We are aware of this point on working on it. Version 2.5.0 is not completely ready yet, but I can send you a beta version by email if you want to try ...
written 11 months ago by vincent.lacroix130
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Answer: A: Kissplice2refgenome does not handle # in the very begining of GTF files
... Dear Thibault, Sorry for answering so late to this post, but yes this issue was corrected a long time ago now. Thanks for reporting it. The current version of k2rg is now 1.2.2 and you are welcome to try it. Best, Vincent ...
written 15 months ago by vincent.lacroix130
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Answer: A: Kissplice2reftranscriptome error : IndexError
... Dear user, This bug should now be solved with version 1.3.3 of k2rt available here: http://kissplice.prabi.fr/tools/kiss2rt/ When using >30 input files to KisSplice, the fasta header gets very long, and blat truncates it when creating .psl files, which causes downstream issues in k2rt. This is n ...
written 15 months ago by vincent.lacroix130
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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 2.3 years ago by vincent.lacroix130 • updated 2.1 years ago by genomax91k
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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 2.6 years ago by vincent.lacroix130
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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 2.7 years ago by vincent.lacroix130
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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 2.8 years ago by vincent.lacroix130
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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 2.9 years ago by vincent.lacroix130
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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 2.9 years ago by vincent.lacroix130

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
Scholar 15 months ago, created an answer that has been accepted. For A: Error in running "diffExpressedVariants" function in kissDE R package
Scholar 4.1 years ago, created an answer that has been accepted. For A: Error in running "diffExpressedVariants" function in kissDE R package

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