User: Chirag Nepal

gravatar for Chirag Nepal
Chirag Nepal2.1k
Reputation:
2,100
Status:
Trusted
Location:
Copenhagen
Website:
http://scholar.google....
Twitter:
ChiragNepal
Last seen:
1 day, 11 hours ago
Joined:
6 years, 10 months ago
Email:
n*************@gmail.com

Posts by Chirag Nepal

<prev • 295 results • page 1 of 30 • next >
1
vote
0
answers
142
views
0
answers
KEGG pathway file for running genome music path-scan
... 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. ...
music kegg written 3 months ago by Chirag Nepal2.1k
0
votes
2
answers
173
views
2
answers
Determine whether it is MSI (micro satellite instability) or not
... 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 ...
msisensors msi written 3 months ago by Chirag Nepal2.1k • updated 3 months ago by lvulliard50
0
votes
3
answers
347
views
3
answers
Comment: C: How to merge chr+strand+coordinate+score from multiple files?
... You can use "**bedtools groupby**" command. Show some example files, will behelpfulr to get precise answer. ...
written 3 months ago by Chirag Nepal2.1k
0
votes
0
answers
157
views
0
answers
Comment: C: Identifying ago2 enriched genes under 2 different conditions
... The authors of Tophat suggest not to use it, but Instead use Kallisto. Nice tutorials. ...
written 4 months ago by Chirag Nepal2.1k
0
votes
1
answer
10k
views
1
answers
Comment: C: Installation of the MuSiC suite on unsupported Linux distributions
... 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 Nepal2.1k
0
votes
0
answers
208
views
0
answers
Comment: C: Tophat2 error: failed to retrieve right/left read for pair
... 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 Nepal2.1k
1
vote
1
answer
217
views
1
answer
Count intron retention reads from BAM files
... 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 ...
intron-retention samtools written 5 months ago by Chirag Nepal2.1k • updated 5 months ago by d-cameron1.9k
2
votes
1
answer
307
views
1
answers
Comment: A: Tophat not installing with Biostar Handbook
... Authors of Tophat paper recommend not to use the software anymore. https://twitter.com/lpachter/status/937055346987712512 ...
written 5 months ago by Chirag Nepal2.1k
0
votes
1
answer
249
views
1
answers
Comment: C: How to determine high-quality somatic mutations
... varscan2, somaticSnipper, virmid, strelka and many more. ...
written 6 months ago by Chirag Nepal2.1k
0
votes
1
answer
389
views
1
answers
Comment: C: Finding zebrafish promoters ENSEMBL
... 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 Nepal2.1k

Latest awards to Chirag Nepal

Good Question 9 weeks 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
Epic Question 3 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.
Good Answer 5 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 6 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 6 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 7 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
Student 9 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 9 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)
Epic Question 12 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
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 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)
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Popular Question 17 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Popular Question 18 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Great Question 20 months ago, created a question with more than 5,000 views. For Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 626 users visited in the last hour