User: TrentGenomics

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Posts by TrentGenomics

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Calling de novo SNPs between two species with KisSplice
... Is there any sources of script to process the mainOutput.tsv file? Eg. summarizing SNPs based on allele frequencies, read counts, and other important descriptors? I only have a year of bioinformatics experience under my belt, and the learning curve has been steep for me in terms of processing more c ...
written 7 weeks ago by TrentGenomics20
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Comment: C: Calling de novo SNPs between two species with KisSplice
... Ah yes, that makes sense to me now. A very good explanation, Thank you very much, Vincent. ...
written 7 weeks ago by TrentGenomics20
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Answer: A: Calling de novo SNPs between two species with KisSplice
... Hi Vincent, Thank you for the detailed explanation, it was extremely useful. Sorry for my misunderstanding, kissDE does suit my needs. I think I am on the right track now. What is the run time of kissDE in your experience? I used kissDE on a cluster previously, and it ran for 10+ days. I was wonde ...
written 7 weeks ago by TrentGenomics20
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Answer: A: Calling de novo SNPs between two species with KisSplice
... Thanks again for getting back to me so quickly. I'm concerned with finding SNPs between conditions, rather than within a condition. For example, if I consider each of my two species a separate condition (species 1 = cond 1, species 2 = cond 2) , then I would like to find SNPs between those conditio ...
written 8 weeks ago by TrentGenomics20
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kissDE error during 'diffExpressedVariants' step: "Error in data.frame..."
... Hi, I'm running kissDE on the results obtained from KisSplice. I used 4 paired-end samples as input for KisSplice, with each of the 8 FQ files totaling ~ 13 gigabytes each. Using R on a high performance computer cluster, kissDE ran for ~12 days, before reaching this error during the 'diffExpress ...
R kissde snp kissplice written 9 weeks ago by TrentGenomics20
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Answer: A: SNPs summaries/statistics from output of KisSplice/KisSplice2RefTranscriptome
... Spent the day learning awk and I think I may be alright with the post analysis. ...
written 12 weeks ago by TrentGenomics20
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Answer: A: KisSplice2RefTranscriptome runtime length
... An update: Finished writing the mainOutput.tsv after ~ 2 days. Still writing the lowQueryCoverageOutput.tsv. ...
written 12 weeks ago by TrentGenomics20
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SNPs summaries/statistics from output of KisSplice/KisSplice2RefTranscriptome
... Hi everyone, I've successfully run the KisSplice/KisSplice2RefTranscriptome workflow to call de novo SNPs from 4 samples. The outputs are printed to large .tsv files. Are there any program packages designed to work with TSV files, similar to VCFtools for VCF files? My experience is novice at b ...
snp rna-seq kissplice written 12 weeks ago by TrentGenomics20
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KisSplice2RefTranscriptome runtime length
... Hi, I'm currently running kissplice2reftranscriptome to predict the impact of SNPs using paired-end reads from 4 samples (8 reads files total, ~45 million bp per file, ~14 gigabytes per file). My 'mergeSNPs.tsv' file is currently ~ 25 megabytes after 24 hrs. What length of runtime should I be exp ...
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Comment: C: CrossMap liftover failed
... Thanks Medhat, I'll give that a try as well. I ran into the same problem where my number of map fails was equal to total entries. May I ask what program you used to generate your chain file, or did you download one? Thanks again. ...
written 3 months ago by TrentGenomics20

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