User: erica

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erica10
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8 months ago
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1 year, 5 months ago
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Posts by erica

<prev • 6 results • page 1 of 1 • next >
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Comment: A: errors running kissplice during de-Bruijn graph
... Thanks again for the quick response. Happy to say we were able to run KisSplice to completion by installing on a different server. Seems likely something in the configuration of the previous server may have interfered with memory allocation at some stage, despite requesting sufficient memory in the ...
written 8 months ago by erica10
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Comment: A: errors running kissplice during de-Bruijn graph
... May thanks for the response. We're running this on a national computing cluster, with fairly substantial memory available. The most we've tried allocating thus far was 105GB and 36 cores. This ran but stopped without reporting an obvious error. However, I see **this error** buried in the output: ...
written 9 months ago by erica10 • updated 8 months ago by genomax71k
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errors running kissplice during de-Bruijn graph
... Hi, I've been trying to run kissplice on my institution's cluster. I run the following script: > kissplice -t 6 -s 1 -k 51 -v -o kiss_results3 --experimental > --max-memory 60000 -r ............ and get a '179971 Bus error', suggesting a memory issue. I've also tried running without --max-m ...
snp rna-seq kissplice written 9 months ago by erica10 • updated 8 months ago by leandro.ishi.lima90
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Comment: C: kissplice SNP output and kissDE runtime
... Thank you Clara. I will try and install the new Bioconductor version of kissDE, and filter the kissplice output to drop the number of SNPs to a more manageable size. Will let you know how things run. Best regards, Erica. ...
written 17 months ago by erica10
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Comment: C: kissplice SNP output and kissDE runtime
... Thanks for the quick response, and the helpful suggestion. Some help with the script would be fantastic - as I have 3 conditions, I would be concerned that removing all SNPs with <10 counts in at least one individual might remove instances of differential expression between two conditions? Best ...
written 17 months ago by erica10
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kissplice SNP output and kissDE runtime
... Hi All, I'm working through the kissplice TWAS pipeline to identify condition-specific SNPs among 3 phenotypes in a wild fish species. Its quite a large dataset, with 4 or 5 replicates per phenotype and 10M paired reads per replicate. Using default parameters and the --experimental algorithm (comma ...
R kissde rna-seq snp kissplice written 18 months ago by erica10 • updated 17 months ago by clara.benoitp10

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