User: Chirag Nepal
Chirag Nepal • 2.2k
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- ChiragNepal
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- Joined:
- 7 years, 4 months ago
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Posts by Chirag Nepal
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... Thanks for the info and nice tool DGIdb.
However, if i have a set of genes (groupA, groupB and so on) as input and want to see enrichment (or p-value) of certain kinds of drugs in these groups. I tried DGIdb, it provides information at the gene level. Any suggestions.
Thank you ! ...
written 7 weeks ago by
Chirag Nepal • 2.2k
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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 4 months ago by
Chirag Nepal • 2.2k
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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 9 months ago by
Chirag Nepal • 2.2k
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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 9 months ago by
Chirag Nepal • 2.2k
• updated
9 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 9 months ago by
Chirag Nepal • 2.2k
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0
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240
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... The authors of Tophat suggest not to use it, but Instead use Kallisto. Nice tutorials. ...
written 10 months ago by
Chirag Nepal • 2.2k
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 11 months ago by
Chirag Nepal • 2.2k
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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 11 months ago by
Chirag Nepal • 2.2k
1
vote
1
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436
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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 11 months ago by
Chirag Nepal • 2.2k
• updated
11 months ago by
d-cameron • 2.0k
2
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1
answer
528
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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 11 months ago by
Chirag Nepal • 2.2k
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Popular Question
10 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
12 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
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
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
4 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?
Great Question
5 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
5 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
5 months ago,
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
7 months ago,
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For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
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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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8 months ago,
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For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
Epic Question
9 months ago,
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For Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
Popular Question
10 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
10 months ago,
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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 Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
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
Popular Question
12 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
12 months ago,
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For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Good Answer
13 months ago,
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For A: help with career decisions: should a PhD in genetics go for another master in bi
Appreciated
13 months ago,
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For A: help with career decisions: should a PhD in genetics go for another master in bi
Student
15 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
15 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
16 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
18 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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