User: b.d237
b.d237 • 100
- Reputation:
- 100
- Status:
- Trusted
- Location:
- National University of Ireland, Galway
- Last seen:
- 1 day, 18 hours ago
- Joined:
- 10 months, 2 weeks ago
- Email:
- b********@hotmail.com
de novo viral miRNA discovery
Posts by b.d237
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... 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.d237 • 100
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... 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.d237 • 100
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... 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.d237 • 100
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... 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 ...
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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.d237 • 100
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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.d237 • 100
0
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2
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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, $vep ...
written 3 months ago by
b.d237 • 100
2
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1
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342
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... Adding:
names(data) <- c("S2Ctrl_7", "WTCtrl_1", "S2Ctrl_8", "WTCtrl_2", "S2Ctrl_9", "WTCtrl_3")
below 'data' did the trick for anyone who has the same problem down the line.. ...
written 4 months ago by
b.d237 • 100
0
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1
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Comment:
C: Tximport > DESeq2 (sample names)
... heatmap image:
https://twitter.com/BarryDigby/status/1068251458343223302 ...
written 4 months ago by
b.d237 • 100
2
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1
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342
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... Using R and tximport, I have read in 6 t_data.ctab files to create a DESeqDataSet by using DESeqDataSetFromTximport.
When plotting heatmaps etc, the sample names are '1', '2', '3', '4', '5', '6'. I suspect it has something to do with reading in the ctab files, when i run **txi$counts** the column ...
written 4 months ago by
b.d237 • 100
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Teacher
10 days ago,
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For A: mireap procedure short tutorial
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For A: Can I get AddOrReplaceReadGroups working for multiple files?
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4 months ago,
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For A: Can I get AddOrReplaceReadGroups working for multiple files?
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For A: Can I get AddOrReplaceReadGroups working for multiple files?
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