User: leandro.ishi.lima
leandro.ishi.lima • 80
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Posts by leandro.ishi.lima
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0
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... Dear Bilal Sarwar,
If KisSplice is taking too much time to run, you could try running the experimental algorithm by adding `--experimental` to your command line. It can be faster, at the cost of using more RAM.
Note also that by using `-s 1` you will get only the Type0a-SNPs, which are single SNP ...
written 1 day ago by
leandro.ishi.lima • 80
0
votes
3
answers
196
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3
answers
... Dear Bilal Sarwar,
If KisSplice is taking too much time to run, you could try running the experimental algorithm by adding `--experimental` to your command line. It can be faster, at the cost of using more RAM.
Note also that by using `-s 1` you will get only the Type0a-SNPs, which are single SNP ...
written 1 day ago by
leandro.ishi.lima • 80
1
vote
1
answer
152
views
1
answers
... 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 3 months ago by
leandro.ishi.lima • 80
2
votes
3
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196
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3
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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 4 months ago by
leandro.ishi.lima • 80
0
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2
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348
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2
answers
... 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 4 months ago by
leandro.ishi.lima • 80
1
vote
2
answers
348
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2
answers
... 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 4 months ago by
leandro.ishi.lima • 80
0
votes
1
answer
300
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1
answers
... 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 months ago by
leandro.ishi.lima • 80
0
votes
1
answer
259
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1
answers
... De nada!
Obrigado pela questão! ...
written 5 months ago by
leandro.ishi.lima • 80
0
votes
1
answer
255
views
1
answers
... 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 5 months ago by
leandro.ishi.lima • 80
0
votes
9
answers
752
views
9
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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 5 months ago by
leandro.ishi.lima • 80
Latest awards to leandro.ishi.lima
Scholar
3 months ago,
created an answer that has been accepted.
For A: Error in running KisSplice_ks_debruijn4
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: Error in running KisSplice_ks_debruijn4
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