User: leandro.ishi.lima
leandro.ishi.lima • 60
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Posts by leandro.ishi.lima
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... 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 1 hour ago by
leandro.ishi.lima • 60
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... 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 10 days ago by
leandro.ishi.lima • 60
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... 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 25 days ago by
leandro.ishi.lima • 60
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... 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 5 weeks ago by
leandro.ishi.lima • 60
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... De nada!
Obrigado pela questão! ...
written 6 weeks ago by
leandro.ishi.lima • 60
0
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139
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... 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 6 weeks ago by
leandro.ishi.lima • 60
0
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... 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 6 weeks ago by
leandro.ishi.lima • 60
0
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500
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... 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 6 weeks ago by
leandro.ishi.lima • 60
0
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1
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170
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... 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 6 weeks ago by
leandro.ishi.lima • 60
2
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500
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... Dear MGlenn,
It seems to me that you might be wishing to find condition-specific (or species-specific) SNPs. You could use perhaps kissDE http://kissplice.prabi.fr/tools/kissDE/ kissDE is a R package, similar to DEseq, but which works on pairs of variants, and tests if a variant is enriched in one ...
written 5 months ago by
leandro.ishi.lima • 60
• updated
4 weeks ago by
Istvan Albert ♦♦ 76k
Latest awards to leandro.ishi.lima
Scholar
20 months ago,
created an answer that has been accepted.
For A: Error in running KisSplice_ks_debruijn4
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