User: Chirag Nepal
Chirag Nepal • 2.1k
- Reputation:
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- Copenhagen
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- http://scholar.google....
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- ChiragNepal
- Last seen:
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- Joined:
- 6 years, 10 months ago
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Posts by Chirag Nepal
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1
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... Hi all,
I am using genome music path-scan to find signifiacntly mutated pathways.
> genome music path-scan --gene-covg-dir gene_covgs --bam-list $bamList
> --pathway-file $pathwayKEGGFile --maf-file $maf --output-file $pathwayOutputFile -bmr 1.8E-6
The program requires KEGG pathway file. ...
written 3 months ago by
Chirag Nepal • 2.1k
0
votes
2
answers
173
views
2
answers
... Hi all,
I used msisensors ( https://github.com/ding-lab/msisensor ) to predict micro satellite instability (MSI).
As an example this patient has 287 MSI events.
> Total_Number_of_Sites Number_of_Somatic_Sites %
>
> 16424 287 1.75
What is the minimum accepted percentage to define wheth ...
written 3 months ago by
Chirag Nepal • 2.1k
• updated
3 months ago by
lvulliard • 50
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votes
3
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... You can use "**bedtools groupby**" command.
Show some example files, will behelpfulr to get precise answer. ...
written 3 months ago by
Chirag Nepal • 2.1k
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157
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... The authors of Tophat suggest not to use it, but Instead use Kallisto. Nice tutorials. ...
written 4 months ago by
Chirag Nepal • 2.1k
0
votes
1
answer
10k
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1
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... Hi Cyriac,
Could you please provide a link to download the KEGG file in the format accepted by Music/Music2.
thanks ! ...
written 4 months ago by
Chirag Nepal • 2.1k
0
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0
answers
208
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... https://twitter.com/lpachter/status/937055346987712512
Why don't you use other better/fast tools like STAR, HiSAT, kallisto and others. ...
written 5 months ago by
Chirag Nepal • 2.1k
1
vote
1
answer
217
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1
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... Hi there,
How to find/filter intron-retained reads from BAM files? Which flag in BAM file describes information about retained intron.
I know there are some tools to find retained intron, but i want to understand how they are represented in BAM files.
When there is an intron retention, portion of ...
written 5 months ago by
Chirag Nepal • 2.1k
• updated
5 months ago by
d-cameron • 1.9k
2
votes
1
answer
307
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1
answers
... Authors of Tophat paper recommend not to use the software anymore.
https://twitter.com/lpachter/status/937055346987712512
...
written 5 months ago by
Chirag Nepal • 2.1k
0
votes
1
answer
249
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1
answers
... varscan2, somaticSnipper, virmid, strelka and many more. ...
written 6 months ago by
Chirag Nepal • 2.1k
0
votes
1
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389
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1
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... Promoter region is kinda arbitrarily defined somewhere between 2/300 bases to 2000 bases upstream of annotated TSS (transcription start sites) from Ensembl/Refseq. So you can extract 2KB region upstream of TSS and get promoter region. CAGE-seq is best way to define TSS, and have a look at this paper ...
written 6 months ago by
Chirag Nepal • 2.1k
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For GATK, SAM file doesn't have any read groups defined in the header
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For Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
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