User: Chirag Nepal
Chirag Nepal • 2.1k
- Reputation:
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- Copenhagen
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- ChiragNepal
- Last seen:
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- Joined:
- 7 years 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 4 months ago by
Chirag Nepal • 2.1k
0
votes
2
answers
243
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 5 months ago by
Chirag Nepal • 2.1k
• updated
5 months ago by
lvulliard • 60
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votes
3
answers
420
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3
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... You can use "**bedtools groupby**" command.
Show some example files, will behelpfulr to get precise answer. ...
written 5 months ago by
Chirag Nepal • 2.1k
0
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178
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... The authors of Tophat suggest not to use it, but Instead use Kallisto. Nice tutorials. ...
written 6 months ago by
Chirag Nepal • 2.1k
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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 6 months ago by
Chirag Nepal • 2.1k
0
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answers
249
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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 6 months ago by
Chirag Nepal • 2.1k
1
vote
1
answer
286
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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 7 months ago by
Chirag Nepal • 2.1k
• updated
7 months ago by
d-cameron • 1.9k
2
votes
1
answer
389
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1
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... Authors of Tophat paper recommend not to use the software anymore.
https://twitter.com/lpachter/status/937055346987712512
...
written 7 months ago by
Chirag Nepal • 2.1k
0
votes
1
answer
304
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1
answers
... varscan2, somaticSnipper, virmid, strelka and many more. ...
written 7 months ago by
Chirag Nepal • 2.1k
0
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1
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470
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1
answers
... 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 8 months ago by
Chirag Nepal • 2.1k
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For Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
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For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
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For GATK, SAM file doesn't have any read groups defined in the header
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