User: sdbaney

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sdbaney0
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Posts by sdbaney

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Creating a gtf annotation file from a FASTA (& bam?) for non-model organism
... or this.... ...
written 20 days ago by sdbaney0
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Comment: C: Creating a gtf annotation file from a FASTA (& bam?) for non-model organism
... ![supertranscripts][1] Did this work? [1]: https://ibb.co/NC9HF89 ...
written 20 days ago by sdbaney0
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Comment: C: Creating a gtf annotation file from a FASTA (& bam?) for non-model organism
... ![enter image description here][1]So I ran supertranscripts (which I am using that FASTA file from it) but the gtf file it gave with it, gave really really odd entries. Here is a snapshot of it: ![supertranscripts.gtf][2] [2]: https://ibb.co/NC9HF89 https://ibb.co/NC9HF89 ...
written 20 days ago by sdbaney0
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Creating a gtf annotation file from a FASTA (& bam?) for non-model organism
... I performed de novo transcriptome assembly. Have the FASTA file that I am using as my reference and also performed alignments of my reads back to that. I have been using stringtie to create gtf files for the differential expression analysis (counting requires a gtf file) but I am trying to do this a ...
rna-seq written 20 days ago by sdbaney0
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Comment: C: Abundance Counting for Non-Model Organism for edgeR
... Thank you, I think that’s what I’m going to end up doing. As stringtie seems to be causing more headache than anticipated. ...
written 25 days ago by sdbaney0
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Abundance Counting for Non-Model Organism for edgeR
... I am working with a non-model organism (no annotated genome or the option to use an annotation file in my abundance counting). I performed de novo transcriptome assembly of the Illumina HiSeq4000 reads. I originally used StringTie as my abundance counter because I didn't need a gtf annotation file ...
rna-seq abundance edger written 26 days ago by sdbaney0 • updated 25 days ago by ATpoint17k
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Answer: A: Condensing dendrogram on heatmap.2
... In the meantime, I adjusted the margins. > heatmap.2(mat_data, Colv=NA, main="Myosin Heatmap", col=my_palette, margins=c(8,5), trace="none", dendrogram="row", scale="row", cexRow=0.5,cexCol=0.8) ![enter image description here][1] [1]: https://ibb.co/10CpDqn ...
written 5 weeks ago by sdbaney0
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Comment: C: DEseq three-group comparison
... wow, thank you so much for your help and manners. ...
written 4 months ago by sdbaney0
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Comment: C: DESEq2 Factor/Level Design
... What I meant was, what sample - which tissue has the higher/lower expression? It doesn't tell me for example, that keel is expressing a value of x. ...
written 4 months ago by sdbaney0
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DESEq2 Factor/Level Design
... I have 3 muscle types 1. keel 2. mantle 3. nuchal I have 3 replicates between each and want to perform differential expression across all 3 to see which transcripts are being significantly differentially expressed. I have been using Cuffdiff because it's simple and the output is nice in that it ha ...
rnas differential expression written 4 months ago by sdbaney0 • updated 4 months ago by blawney10

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