User: leandro.ishi.lima
leandro.ishi.lima • 20
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Posts by leandro.ishi.lima
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... Dear cc86,
Could you describe the file you generated? The events.txt file output by kissplice2refgenome works fine when given to the software, but it does not fit your needs?
Thanks!
++ ...
written 3 months ago by
leandro.ishi.lima • 20
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Answer:
A: kissplice on TWAS analysis
... Hello Tom,
Sorry for the delay on answering you.
>Is there any upper bound for the number of samples for kissplice?
No, did you have any problem when running it with your large number of samples? Surely, if your dataset is huge, you will probably need more disk, CPU time and RAM. It is also a ...
written 4 months ago by
leandro.ishi.lima • 20
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... Dear cc86,
The page http://kissplice.prabi.fr/sknsh/ is outdated (our fault). The updated page for the pipeline you are looking for can be found here: http://kissplice.prabi.fr/pipeline_ks_farline/ . Thanks for the report, we will do a redirecting of http://kissplice.prabi.fr/sknsh/ to http://kissp ...
written 5 months ago by
leandro.ishi.lima • 20
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... Dear Chiara,
Thanks for reporting this bug.
Could you send us an input file, with your command-line, so that we can debug?
Thanks !
Kind regards. ...
written 6 months ago by
leandro.ishi.lima • 20
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... Hello,
Maybe this is a command-line error, I am not sure. Could you please try the following run:
kissplice2refgenome -a myAnnotationsFile.gtf -o myOutputFile myPSLfile.psl
If this still does not work, maybe it is a good idea to try with a .sam file. Transform your psl to sam using samtools/m ...
written 7 months ago by
leandro.ishi.lima • 20
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... Hello yoyofangliu,
Were you eventually able to make KisSplice run? We still wait your response.
Thanks. ...
written 11 months ago by
leandro.ishi.lima • 20
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... Hello,
According to https://gcc.gnu.org/projects/cxx-status.html#cxx11 , GCC 4.8.1 was the first feature-complete implementation of the 2011 C++ standard. Is it possible for you to upgrade your GCC to 4.8.1 or higher?
Thanks for the report. ...
written 12 months ago by
leandro.ishi.lima • 20
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... Hello,
We have three options to try to narrow down the reasons why KisSplice is failing to process your data:
1) Check if the compilation and installation are fine: you can do this by entering the directory you compiled KisSplice (i.e. the directory that you ran cmake and make) and running "make te ...
written 13 months ago by
leandro.ishi.lima • 20
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... Dear Chiara,
Could you post the full output and the error log (if you redirected the error stream) please? If you ran in verbose mode (-v), it is even better!
Thanks. ...
written 13 months ago by
leandro.ishi.lima • 20
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... Hello,
Could you, please, give me an overview of what is going to be taught on GATB programming day? Will we have only the basic things that are covered in the examples directory of GATB's core, or will we have some other stuff?
Thank you very much.
...
written 16 months ago by
leandro.ishi.lima • 20
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12 months ago,
created an answer that has been accepted.
For A: Error in running KisSplice_ks_debruijn4
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