User: Barry Digby
Barry Digby • 420
- Reputation:
- 420
- Status:
- Trusted
- Location:
- National University of Ireland, Galway
- Twitter:
- @BarryDigby
- Last seen:
- 10 hours ago
- Joined:
- 2 years, 2 months ago
- Email:
- b********@hotmail.com
Currently attempting to get to the bottom of how circRNA - miRNA interactions are predicted and more importantly, ranked.
Posts by Barry Digby
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... Perfect, thanks Pierre. Ran into the same problem using a container.
`snpEff download GRCh37.75 -dataDir /data/snpEff`
@abe add the `-dataDir` flag . . . ...
written 2 days ago by
Barry Digby • 420
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Answer:
A: RNA seq data analysis
... This video should be what you want:
[#16 Lockdown Learning Bioinformatics-along: Downloading from the SRA][1]
[1]: https://www.youtube.com/watch?v=RSPaaSfA8DI ...
written 23 days ago by
Barry Digby • 420
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... When saving the normalized counts in R set `quote = FALSE` .
Or just remove them using sed `sed 's/"//g' your_file.gct > no_quotes.gct` ...
written 25 days ago by
Barry Digby • 420
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... Hi Kevin,
I wanted to add on a quick side question to this thread (I don't think it warrants a new post, still discussing sample variation present in TCGA-PRAD DE analysis)
When creating the design for DESeq2, the simplest way to do it is `design = ~ Condition` where condition has tumor/normal in ...
written 5 weeks ago by
Barry Digby • 420
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... Hi Bruce,
I've had a spot of bother making the image. I have replaced the `%post` with my github repo but `singularity build` returns `ERROR: 'Bootstrap' type not supported: library`. I also went to the [page][1] where the container is hosted and tried to install via `singularity pull`, but it ret ...
written 6 weeks ago by
Barry Digby • 420
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... Hi Bruce,
Yep, I derived the local solution (answer below) from a suggestion on the github page linked. Cool, I did not know you could create a container from a `.yml` file, could you share the singularity call used to build the container? I am keen on making this pipeline reproducible , +1 for po ...
written 7 weeks ago by
Barry Digby • 420
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... It worked? great! So the solution was to remake the `arf` file? ...
written 7 weeks ago by
Barry Digby • 420
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... sorry, I must have had it confused with mireap. are you sure the sequence lengths are all above 17? you might have to dig deeper into that.
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' test.fa > lenghts.txt
and parse output ...
written 8 weeks ago by
Barry Digby • 420
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... Take a look at this tutorial https://www.biostars.org/p/213088/#373944
You will need to split the fasta headers so that the collapsed read counts have a space separating the ID and count using `sed`
>seq_1_x1
CTTATAGTGTAAGGTGGAATGAAG
to
>seq_1_x 1
CTTATAGTGTAAGGTGGAATGAAG ...
written 8 weeks ago by
Barry Digby • 420
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... I see, I'm a fan of using
source /home/Anaconda3/4.4.0/etc/profile.d/conda.sh
conda activate env-name
Many ways to die in the west as my sys admin says!
The `PATH` method is for nextflow specifically :) ...
written 8 weeks ago by
Barry Digby • 420
Latest awards to Barry Digby
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For Tximport > DESeq2 (sample names)
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: Can I get AddOrReplaceReadGroups working for multiple files?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Tximport > DESeq2 (sample names)
Student
5 months ago,
asked a question with at least 3 up-votes.
For Counting Gene Clusters from Antismash Output
Popular Question
7 months ago,
created a question with more than 1,000 views.
For GATK Panel Of Normals (PoN)
Teacher
8 months ago,
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For A: mireap procedure short tutorial
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9 months ago,
created a question with more than 1,000 views.
For GATK Panel Of Normals (PoN)
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Appreciated
10 months ago,
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For A: mireap procedure short tutorial
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12 months ago,
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For A: Can I get AddOrReplaceReadGroups working for multiple files?
Teacher
16 months ago,
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For A: mireap procedure short tutorial
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16 months ago,
created an answer that has been accepted.
For A: Can I get AddOrReplaceReadGroups working for multiple files?
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20 months ago,
created an answer that has been accepted.
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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