User: leandro.ishi.lima

Reputation:
80
Status:
Trusted
Location:
Last seen:
10 hours ago
Joined:
2 years, 7 months ago
Email:
l****************@gmail.com

Posts by leandro.ishi.lima

<prev • 25 results • page 1 of 3 • next >
0
votes
3
answers
196
views
3
answers
Answer: A: Kissplice: Problem getting SNPs in test data
... 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.lima80
0
votes
3
answers
196
views
3
answers
Comment: C: Kissplice: Problem getting SNPs in test data
... 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.lima80
1
vote
1
answer
152
views
1
answers
Answer: A: error in downloading kissplice
... 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.lima80
2
votes
3
answers
196
views
3
answers
Answer: A: Kissplice: Problem getting SNPs in test data
... 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.lima80
0
votes
2
answers
348
views
2
answers
Comment: C: kissplice SNP output and kissDE runtime
... 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.lima80
1
vote
2
answers
348
views
2
answers
Answer: A: kissplice SNP output and kissDE runtime
... 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.lima80
0
votes
1
answer
300
views
1
answers
Answer: A: Empty output file with Kissplice2refgenome
... 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.lima80
0
votes
1
answer
259
views
1
answers
Comment: C: Error before creating De Bruin Graphs
... De nada! Obrigado pela questão! ...
written 5 months ago by leandro.ishi.lima80
0
votes
1
answer
255
views
1
answers
Answer: A: Kissplice "Finding BCCs" and no output fa or tsv files
... 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.lima80
0
votes
9
answers
752
views
9
answers
Comment: C: Calling de novo SNPs between two species with KisSplice
... 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.lima80

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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1361 users visited in the last hour