User: Chloe

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Chloe0
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Posts by Chloe

<prev • 5 results • page 1 of 1 • next >
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Duplicate gene names in count matrix from GTF file that can't be parsed to edgeR
... Hi all, I'm having an issue with duplicate gene names/IDs which are interfering with parsing my count matrix to edgeR. I have a GFF3 file which I converted to GTF using: gffread my.gff3 -T -o my.gtf I am able to produce a count matrix using this gtf file thorugh HTSeq. However, when I try ...
genome count matrix rna-seq edger dge written 8 months ago by Chloe0 • updated 6 months ago by ytian0
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Comment: C: Normalizing for RNA abundance across replicates from a time course
... Awesome thanks I'll give this a go ...
written 8 months ago by Chloe0
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Normalizing for RNA abundance across replicates from a time course
... Hi all, I am trying to normalize my read counts for differential gene expression with edgeR I have a set of 21 bam files from aligning my reads to a genome, corresponding to 3 replicates at each of my 7 time points. I would like to do DGE using edgeR, but first I need to normalize for RNA abundan ...
normalization rna abundance edger rsem rna-seq written 8 months ago by Chloe0 • updated 8 months ago by Jacob Warner500
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Comment: C: How to trim adapters and remove polyA tails from QuantSeq 3' FWD data
... Thanks I'll try that. Will that only remove poly As of that exact length from the end of the read? The reads are short and generated towards the 3' end, so some of the poly A tails seem to be in the middle of the read ...
written 9 months ago by Chloe0
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How to trim adapters and remove polyA tails from QuantSeq 3' FWD data
... I am trying to work out the best way to trim poly A tails of variable length from the 3' end of my data and if possible also remove adapters and other contaminating sequence at the same time from the 5' end. My data is 75 bp single end. Libraries were prepared using the QuantSeq 3' FWD kit and se ...
poly-a tails rna-seq trim quantseq written 9 months ago by Chloe0

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