User: dec986

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dec98690
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Posts by dec986

<prev • 84 results • page 1 of 9 • next >
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MSigDB gene set enrichment analysis
... 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 ...
gene ontology gsea written 8 days ago by dec98690
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Comment: C: [Opinion] - What alignment software do you use?
... 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 dec98690
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Answer: A: [Opinion] - What alignment software do you use?
... 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 dec98690
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Comment: C: Differentially methylated regions: Easy & Fast Identification and ANnoTation
... 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 dec98690
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Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
... ## 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 ...
dna methylation tutorial dmr written 8 weeks ago by dec98690
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Choice of Gene Length in TPM Calculations
... 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 ...
tpm rna-seq written 8 weeks ago by dec98690
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Creating genome alignment
... 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 ...
star rna-seq written 10 weeks ago by dec98690 • updated 10 weeks ago by lshepard130
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Comment: C: STAR Alignment Score reduced after trimming
... great, thanks, I have to let my colleagues know. We're comparing several different RNA-Seq pipelines. ...
written 10 weeks ago by dec98690
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Comment: C: STAR Alignment Score reduced after trimming
... thank you! who is "our"? ...
written 10 weeks ago by dec98690
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STAR Alignment Score reduced after trimming
... 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 ...
star rna-seq written 10 weeks ago by dec98690 • updated 10 weeks ago by Devon Ryan78k

Latest awards to dec986

Teacher 23 days ago, created an answer with at least 3 up-votes. For A: [Opinion] - What alignment software do you use?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 3 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Scholar 5 months ago, created an answer that has been accepted. For A: Alignment with STAR produces unique bam files, but identical output from bedtool
Popular Question 13 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 13 months ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
Popular Question 13 months ago, created a question with more than 1,000 views. For Conversion between .bedGraph or .bw to 7-column format
Popular Question 13 months ago, created a question with more than 1,000 views. For edgeR: no residual df: Cannot estimate dispersion
Supporter 13 months ago, voted at least 25 times.
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq2 comparison failure
Scholar 23 months ago, created an answer that has been accepted. For A: Alignment with STAR produces unique bam files, but identical output from bedtool

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