User: dec986
dec986 • 90
- Reputation:
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- United States
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- 1 day, 14 hours ago
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- 3 years, 2 months ago
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Posts by dec986
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... Hello,
I have been using Gorilla gene ontology with help from a great post on BioStars https://www.biostars.org/p/70064/
However, a colleague wishes to use 8 separate analyses listed on http://software.broadinstitute.org/gsea/msigdb/index.jsp for each comparison in our project
I have a *lot* of a ...
written 8 days ago by
dec986 • 90
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... For my particular purpose, I downloaded GSE96075 and compared STAR against HISAT2. STAR's extra reads could indeed be false positives, but I had no way of verifying that. I was satisfied because the read length was fairly long (~198 nucleotides) so the slightly higher mismatch mean was acceptable. ...
written 21 days ago by
dec986 • 90
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... Through my own experimentation, STAR gives the best balance between selectivity and sensitivity. However, the mismatch rate is a little higher than HISAT2. I don't think that this is significant. HISAT2 comes as 2nd place, as it gets far fewer reads (sometimes tens of thousands with similar setti ...
written 23 days ago by
dec986 • 90
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... how do you mean 'truncated'? could you provide a specific example, so if something is wrong, I can fix it? ...
written 7 weeks ago by
dec986 • 90
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... ## Introduction ##
I would like to show how to use a new program to identify differentially methylated regions (DMRs) from bisulfite sequencing data, whether whole-genome or RRBS. This tutorial won't be very long, as the program is remarkably easy to use, and doesn't require learning a programming ...
written 8 weeks ago by
dec986 • 90
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... Hello,
I am attempting to convert read count output from STAR into TPM.
However, there is some ambiguity in what gene length to use.
from Gencode27:
chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pse ...
written 8 weeks ago by
dec986 • 90
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... Hello,
I am confused about the difference between `GRCh37.p13.genome.fa` (767 MB, http://www.gencodegenes.org/releases/19.html) and `GRCh37.primary_assembly.genome.fa` (830 MB http://www.gencodegenes.org/releases/27lift37.html) which is lifted from Gencode release 27. I want to use the most recent ...
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... great, thanks, I have to let my colleagues know. We're comparing several different RNA-Seq pipelines. ...
written 10 weeks ago by
dec986 • 90
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... thank you! who is "our"? ...
written 10 weeks ago by
dec986 • 90
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5 follow
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... Hello,
I'm comparing three different QC tools (trimgalore, trimmomatic, & bbduk) and then seeing how STAR alignments are affected by all of them, comparing against a noQC run. Specifically, I am comparing the "AS" and "nM" fields in the BAM file. I figured that the alignment scores should inc ...
written 10 weeks ago by
dec986 • 90
• updated
10 weeks ago by
Devon Ryan ♦ 78k
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