User: leandro.ishi.lima
leandro.ishi.lima • 80
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Posts by leandro.ishi.lima
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Answer:
A: Error in running KisSplice
... Dear 963786304,
The error probably indicates that KisSplice was not able to locate your input file.
It is possible that you were not located in the directory which contained your data when you launched KisSplice.
I suggest you change directory and retry, or use the full path to your data file in th ...
written 8 days ago by
leandro.ishi.lima • 80
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Answer:
A: error while Kissplice run
... Dear KG,
I am redirecting your doubt to the other maintainers, but could you give us more details on the pipeline you are using to call SNPs from transcriptome data, if possible with the command lines?
We also propose the following pipeline: http://kissplice.prabi.fr/TWAS/ for SNP calling from RNA ...
written 20 days ago by
leandro.ishi.lima • 80
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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 8 weeks ago by
leandro.ishi.lima • 80
0
votes
3
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268
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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 8 weeks ago by
leandro.ishi.lima • 80
1
vote
1
answer
195
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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 5 months ago by
leandro.ishi.lima • 80
2
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answers
... 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 5 months ago by
leandro.ishi.lima • 80
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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 6 months ago by
leandro.ishi.lima • 80
1
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2
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405
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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 6 months ago by
leandro.ishi.lima • 80
0
votes
1
answer
334
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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 7 months ago by
leandro.ishi.lima • 80
0
votes
1
answer
293
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1
answers
... De nada!
Obrigado pela questão! ...
written 7 months ago by
leandro.ishi.lima • 80
Latest awards to leandro.ishi.lima
Scholar
5 months ago,
created an answer that has been accepted.
For A: Error in running KisSplice_ks_debruijn4
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Error in running KisSplice_ks_debruijn4
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