User: b.d237

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b.d237100
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National University of Ireland, Galway
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de novo viral miRNA discovery

Posts by b.d237

<prev • 22 results • page 1 of 3 • next >
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Answer: A: prediction of viral miRNAs by Vmir analyzer...
... Contacted the developer Adam Grundhoff, its available here: [VMir Analyzer][1] [1]: http://virus-genomics.org/software/vmir/vmir.html ...
written 5 days ago by b.d237100
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Answer: A: mireap procedure short tutorial
... Hopefully this post helps people who need help with MIREAP, as the error messages are non existent and as far as I can see from google searches, no forum board goes into this depth. Installing miRDeep2 and MIREAP is a pain in the @$$ but I'm not covering installation in this post. I used miRDeep2 ...
written 10 days ago by b.d237100
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Comment: C: miRDeep2 installation 'make_html.pl'
... Thanks for the response, aforementioned sysadmin corrected it by adding use lib '/home/bdigby/bin/mirdeep2/lib/'; to the header of the perl script and it worked :) ...
written 17 days ago by b.d237100
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miRDeep2 installation 'make_html.pl'
... Hi guys, I have been following the installation steps for miRDeep2 outlined here: [https://github.com/rajewsky-lab/mirdeep2.][1] I am stuck on the final step of testing installation, testing the make_html.pl script. The error I receive is: Can't locate PDF/API2.pm in @INC (@INC contains: PER ...
perl pdf::api2 mirdeep2 written 17 days ago by b.d237100 • updated 17 days ago by RamRS21k
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Comment: C: Convertion Of Gff3 To Gtf
... Could you please expand on this? I have just used Cufflinks v2.2.1 for gffread. The output GTF file looks fine, checking against specifications stated here: https://www.ensembl.org/info/website/upload/gff.html. ...
written 25 days ago by b.d237100
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Comment: C: How to convert vcf to MAF ?
... post the error message you're getting if it's still not working ...
written 3 months ago by b.d237100
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Answer: A: How to convert vcf to MAF ?
... When using **vcf2maf.pl** you have to edit the paths of files in the script. Following up with what **Raony Guimarães** said, you will need VEP, and you will also need to specify its path: ***nano vcf2maf.pl :*** # Set any default paths and constants ... my ( $vep_path, $vep_data, $vep ...
written 3 months ago by b.d237100
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Answer: A: Tximport > DESeq2 (sample names)
... Adding: names(data) <- c("S2Ctrl_7", "WTCtrl_1", "S2Ctrl_8", "WTCtrl_2", "S2Ctrl_9", "WTCtrl_3") below 'data' did the trick for anyone who has the same problem down the line.. ...
written 4 months ago by b.d237100
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Comment: C: Tximport > DESeq2 (sample names)
... heatmap image: https://twitter.com/BarryDigby/status/1068251458343223302 ...
written 4 months ago by b.d237100
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Tximport > DESeq2 (sample names)
... Using R and tximport, I have read in 6 t_data.ctab files to create a DESeqDataSet by using DESeqDataSetFromTximport. When plotting heatmaps etc, the sample names are '1', '2', '3', '4', '5', '6'. I suspect it has something to do with reading in the ctab files, when i run **txi$counts** the column ...
tximport deseq2 rna-seq written 4 months ago by b.d237100

Latest awards to b.d237

Teacher 10 days ago, created an answer with at least 3 up-votes. For A: mireap procedure short tutorial
Scholar 10 days ago, created an answer that has been accepted. For A: Can I get AddOrReplaceReadGroups working for multiple files?
Scholar 4 months ago, created an answer that has been accepted. For A: Can I get AddOrReplaceReadGroups working for multiple files?
Scholar 5 months ago, created an answer that has been accepted. For A: Can I get AddOrReplaceReadGroups working for multiple files?
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