User: leandro.ishi.lima

Reputation:
30
Status:
New User
Location:
Last seen:
2 weeks, 5 days ago
Joined:
1 year, 11 months ago
Email:
l****************@gmail.com

Posts by leandro.ishi.lima

<prev • 13 results • page 1 of 2 • next >
1
vote
8
answers
227
views
8
answers
Answer: A: Calling de novo SNPs between two species with KisSplice
... 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 o ...
written 22 days ago by leandro.ishi.lima30
0
votes
1
answer
171
views
1
answers
Answer: A: kissDE error during 'diffExpressedVariants' step: "Error in data.frame..."
... Dear TrentGenomics, In order to debug better this error (which we have not seen before), could you please: 1) Post the command line you used for KisSplice and kissDE? 2) What your "species" vector contain? 3) Print the head of your "snp" data.frame? 4) Did you do the quality control step of kis ...
written 25 days ago by leandro.ishi.lima30
0
votes
8
answers
227
views
8
answers
Answer: A: Calling de novo SNPs between two species with KisSplice
... Dear MGlenn, The command you described would call SNPs between all combinations of cond1, replicate 1, replicate 2, cond2, replicate 1, replicate 2 etc. In KisSplice, firstly the bubbles corresponding to SNPs are found, and only after they are quantified according to conditions, replicates, etc. Th ...
written 26 days ago by leandro.ishi.lima30
0
votes
2
answers
330
views
2
answers
Comment: C: kiss2refgenome - fail in read kiss2refgenome using kissDE
... 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 7 months ago by leandro.ishi.lima30
0
votes
1
answer
321
views
1
answers
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 8 months ago by leandro.ishi.lima30
0
votes
2
answers
330
views
2
answers
Answer: A: kiss2refgenome - fail in read kiss2refgenome using kissDE
... 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 8 months ago by leandro.ishi.lima30
0
votes
2
answers
516
views
2
answers
Answer: A: Error in running kissplice2reftranscriptome
... 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 10 months ago by leandro.ishi.lima30
0
votes
1
answer
454
views
1
answers
Answer: A: troubleshooting: error on run of kissplice2refgenome
... 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 11 months ago by leandro.ishi.lima30
0
votes
0
answers
610
views
0
answers
Comment: A: error during installationi of KisSplice
... Hello yoyofangliu, Were you eventually able to make KisSplice run? We still wait your response. Thanks. ...
written 15 months ago by leandro.ishi.lima30
0
votes
0
answers
610
views
0
answers
Comment: C: error during installationi of KisSplice
... 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 16 months ago by leandro.ishi.lima30

Latest awards to leandro.ishi.lima

Scholar 16 months ago, created an answer that has been accepted. For A: Error in running KisSplice_ks_debruijn4

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 971 users visited in the last hour