User: jpcchoy

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jpcchoy0
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Posts by jpcchoy

<prev • 13 results • page 1 of 2 • next >
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Comment: C: How to include geneIDs in colData and countData format in DESeq2?
... Thanks so much! This worked :) ...
written 4 months ago by jpcchoy0
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How to include geneIDs in colData and countData format in DESeq2?
... Hi everyone, I'm trying to analyse a bunch of ribo-seq samples using DESeq2. I know that `ncol(countData) == nrow(colData)` should evaluate TRUE. But I don't know how to input GeneIDs in this case. Currently, my colData looks as follows: > coldata Sample Treatment [1,] "cts ...
deseq2 rna-seq written 4 months ago by jpcchoy0 • updated 4 months ago by swbarnes27.0k
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Way to do differential gene expression analysis without writing Rscripts?
... Hi, everyone. I have generated gene count tables from Ribo-Seq data across four different treatment conditions using featureCounts, and would like to work out differential gene expression across the four conditions. I had hoped to use DESeq2, but I've found it difficult as I am not sufficiently com ...
rna-seq differential expression written 4 months ago by jpcchoy0 • updated 4 months ago by Charles Warden7.5k
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Comment: C: What is DESeq2 factor?
... Ah, figured it out. No worries. ...
written 4 months ago by jpcchoy0
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Comment: C: What is DESeq2 factor?
... Yes, exactly. I understand what a factor is in R, but I don't understand what a factor is in the specific context of DESeq2. ...
written 4 months ago by jpcchoy0
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Mapping aligned reads to UTRs
... Hi everyone, I'm trying to work out which of my aligned reads in a sorted BAM file map to UTRs. I have a text file with transcript and CDS coordinates as follows: **name chrom strand txStart txEnd cdsStart cdsEnd ** ENST00000371007.6 chr1 - 67092164 67231852 67093004 67127240 ENST00000371006.5 ...
cds alignment utr rna-seq written 5 months ago by jpcchoy0 • updated 5 months ago by Ace70
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Comment: C: Finding Ribo-seq reads in annotated UTRs
... Context: Process BAM file rsemout.transcript.sorted.bam... Single-end reads are included. Assign alignments to features... Segmentation fault (core dumped) ...
written 6 months ago by jpcchoy0
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Comment: C: Finding Ribo-seq reads in annotated UTRs
... I just tried this a few times with different parameters, and every time I get a Segmentation fault (core dumped) Do you know why this might be? ...
written 6 months ago by jpcchoy0
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Comment: C: Finding Ribo-seq reads in annotated UTRs
... Yes! I had not noticed that h.mon, but you're absolutely right. Unfortunately, I've run htseq-count in the following way and all of my sequences map to 0 features... htseq-count -f bam -r pos sorted.bam gencode.v30.annotation.gtf All I get is this: __no_feature 1993081 __ambiguous 0 ...
written 6 months ago by jpcchoy0
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Comment: C: Finding Ribo-seq reads in annotated UTRs
... And I can provide more details if helpful! ...
written 6 months ago by jpcchoy0

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