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:
- 9 hours ago
- Joined:
- 7 years, 2 months ago
- Email:
- n*************@gmail.com
Posts by Chirag Nepal
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... To predict pri-miRNA sequence, sequencing data (RNA-seq, histone chip-seq, CAGE-seq and other data) is necessary, and very difficult to predict simply based on DNA sequence.
Here is one paper https://www.ncbi.nlm.nih.gov/pubmed/26673698
Of course there are other papers which have implemented simila ...
written 8 weeks ago by
Chirag Nepal • 2.1k
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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 7 months ago by
Chirag Nepal • 2.1k
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... 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 7 months ago by
Chirag Nepal • 2.1k
• updated
7 months ago by
lvulliard • 60
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... You can use "**bedtools groupby**" command.
Show some example files, will behelpfulr to get precise answer. ...
written 8 months ago by
Chirag Nepal • 2.1k
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... The authors of Tophat suggest not to use it, but Instead use Kallisto. Nice tutorials. ...
written 8 months ago by
Chirag Nepal • 2.1k
0
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1
answer
11k
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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 9 months ago by
Chirag Nepal • 2.1k
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314
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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 9 months ago by
Chirag Nepal • 2.1k
1
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1
answer
367
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1
answer
... 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 9 months ago by
Chirag Nepal • 2.1k
• updated
9 months ago by
d-cameron • 1.9k
2
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1
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457
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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 9 months ago by
Chirag Nepal • 2.1k
0
votes
1
answer
377
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1
answers
... varscan2, somaticSnipper, virmid, strelka and many more. ...
written 10 months ago by
Chirag Nepal • 2.1k
Latest awards to Chirag Nepal
Popular Question
17 days ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
28 days ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
9 weeks ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Great Question
3 months ago,
created a question with more than 5,000 views.
For Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: help with career decisions: should a PhD in genetics go for another master in bi
Popular Question
3 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
Good Question
6 months ago,
asked a question that was upvoted at least 5 times.
For GATK, SAM file doesn't have any read groups defined in the header
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
Epic Question
7 months ago,
created a question with more than 10,000 views.
For Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
Appreciated
8 months ago,
created a post with more than 5 votes.
For A: help with career decisions: should a PhD in genetics go for another master in bi
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
Good Answer
9 months ago,
created an answer that was upvoted at least 5 times.
For A: help with career decisions: should a PhD in genetics go for another master in bi
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Good Answer
11 months ago,
created an answer that was upvoted at least 5 times.
For A: help with career decisions: should a PhD in genetics go for another master in bi
Appreciated
11 months ago,
created a post with more than 5 votes.
For A: help with career decisions: should a PhD in genetics go for another master in bi
Student
13 months ago,
asked a question with at least 3 up-votes.
For GATK, SAM file doesn't have any read groups defined in the header
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Epic Question
16 months ago,
created a question with more than 10,000 views.
For GATK, SAM file doesn't have any read groups defined in the header
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