User: leandro.ishi.lima

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Posts by leandro.ishi.lima

<prev • 23 results • page 1 of 3 • next >
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Answer: A: error in downloading kissplice
... Dear Archie, I guess it was a downtime on the FTP server, since now it seems to be working. I was able to download KisSplice2RefTranscriptome version 1.3.2 when writing this message. Could you please retry and check if it is working for you now? Kind regards. ...
written 6 weeks ago by leandro.ishi.lima70
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Answer: A: Kissplice: Problem getting SNPs in test data
... Dear WeepingMeadow, Unfortunately our test dataset only includes one alternative splicing event, which is found in file results_reads1_reads2_k41_coherents_type_1.fa. No SNPs are present, thus files results_reads1_reads2_k41_coherents_type_0a.fa and results_reads1_reads2_k41_coherents_type_0b.fa ar ...
written 8 weeks ago by leandro.ishi.lima70
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Comment: C: kissplice SNP output and kissDE runtime
... Dear Erica, Did the Bioconductor version of kissDE work for you? Here you can find a very simple script to filter out some lowly-expressed bubbles: https://www.dropbox.com/s/6zfx946kqo7yxfb/remove_lowly_covered_bubbles.py?dl=1 You call it as: python remove_lowly_covered_bubbles.py where: ...
written 9 weeks ago by leandro.ishi.lima70
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Answer: A: kissplice SNP output and kissDE runtime
... Dear Erica, We are investigating the kissDE performance to answer you. What I might help you right now is on removing SNPS with <10 reads mapped in at least one sample, just after running KisSplice. You could process the fields ...|C1_X|C2_Y|C3_Z|... in the header of the SNPs and remove t ...
written 11 weeks ago by leandro.ishi.lima70
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Answer: A: Empty output file with Kissplice2refgenome
... Hello, If all of your snps were in the notmappedread file, there could have some reasons (see section 3.1.2 of Kissplice2refgenome's manual: ftp://pbil.univ-lyon1.fr/pub/logiciel/kissplice/tools/kissplice2refgenome_userguide.pdf ): 1) the mapper did not manage to map the SNPs; 2) If you are working ...
written 3 months ago by leandro.ishi.lima70
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Comment: C: Error before creating De Bruin Graphs
... De nada! Obrigado pela questão! ...
written 3 months ago by leandro.ishi.lima70
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Answer: A: Kissplice "Finding BCCs" and no output fa or tsv files
... Dear audrahuffmeyer, There is a common problem in this step if your graph is too large and your stack size is not sufficiently large for the several calls of a recursive algorithm. To solve this problem, try to run (in Unix systems): ulimit -s unlimited before running KisSplice. If you are u ...
written 3 months ago by leandro.ishi.lima70
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Comment: C: Calling de novo SNPs between two species with KisSplice
... Dear TrentGenomics, Do you have any more doubts or are all of them solved? Did kissDE suit your needs or your question needs another tool? Thanks. ...
written 3 months ago by leandro.ishi.lima70
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Answer: A: Calling de novo SNPs between two species with KisSplice
... Dear TrentGenomics, Sorry for the late answer, we did not get notifications for your replies. Does kissDE finished running? I guess you were on the right track, once you get kissDE output you might have your answer. You can try to process .tsv files using spreadsheet processors like Excel and Lib ...
written 3 months ago by leandro.ishi.lima70
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Answer: A: Error before creating De Bruin Graphs
... Dear vshiv, Sorry for the late reply. It could be that KisSplice is trying to create temporary files in the /tmp folder, and this partition might not be too big. You can override which temp folder to use by passing the parameter -d: -d : Specific directory (absolute path) where to build tempor ...
written 3 months ago by leandro.ishi.lima70

Latest awards to leandro.ishi.lima

Scholar 6 weeks ago, created an answer that has been accepted. For A: Error in running KisSplice_ks_debruijn4
Scholar 22 months ago, created an answer that has been accepted. For A: Error in running KisSplice_ks_debruijn4

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