User: TrentGenomics

gravatar for TrentGenomics
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5 days, 17 hours ago
Joined:
4 months, 3 weeks ago
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m********@trentu.ca

Posts by TrentGenomics

<prev • 32 results • page 1 of 4 • next >
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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 5 days ago by TrentGenomics20 • updated 3 days ago by leandro.ishi.lima20
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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 23 days 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 24 days 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 24 days 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 6 weeks ago by TrentGenomics20
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Comment: C: GMAP error - Problem Sequence: TRINITY_DN422143_c0_g1_i1 (301 bp)
... Hi genomax. There is only one instance of that Trinity accession in my fasta file. ...
written 6 weeks ago by TrentGenomics20
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GMAP error - Problem Sequence: TRINITY_DN422143_c0_g1_i1 (301 bp)
... Hello, I'm using GMAP-2017-09-11 as part of the RECOT (read coordinate transformer; http://sesejun.github.io/recot/ ; https://scfbm.biomedcentral.com/articles/10.1186/1751-0473-8-6) pipeline to transform the coordinates of a transcriptome assembly to the coordinates of the mouse genome (Mus_muscul ...
alignment written 6 weeks ago by TrentGenomics20 • updated 6 weeks ago by WouterDeCoster23k
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Comment: C: Very high alignment rate with bowtie2
... I do agree Macspider, but I've seen many examples where assembly quality checks by way of read representation do not exceed the range of 70-85 %. ...
written 9 weeks ago by TrentGenomics20
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Answer: A: Very high alignment rate with bowtie2
... These are just the tips I was looking for. I'm going to play around with the raw and trimmed reads with bowtie2 and have a look at the alignment stats. Thanks again, Kevin! I appreciate it. ...
written 9 weeks ago by TrentGenomics20

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