User: Chirag Nepal

gravatar for Chirag Nepal
Chirag Nepal2.1k
Reputation:
2,130
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Location:
Copenhagen
Website:
http://scholar.google....
Twitter:
ChiragNepal
Last seen:
14 hours ago
Joined:
7 years ago
Email:
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Posts by Chirag Nepal

<prev • 295 results • page 1 of 30 • next >
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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 4 months ago by Chirag Nepal2.1k
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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 5 months ago by Chirag Nepal2.1k • updated 5 months ago by lvulliard60
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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 5 months ago by Chirag Nepal2.1k
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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 6 months ago by Chirag Nepal2.1k
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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 6 months ago by Chirag Nepal2.1k
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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 6 months ago by Chirag Nepal2.1k
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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 7 months ago by Chirag Nepal2.1k • updated 7 months ago by d-cameron1.9k
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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 7 months ago by Chirag Nepal2.1k
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Comment: C: How to determine high-quality somatic mutations
... varscan2, somaticSnipper, virmid, strelka and many more. ...
written 7 months ago by Chirag Nepal2.1k
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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 8 months ago by Chirag Nepal2.1k

Latest awards to Chirag Nepal

Good Question 3 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
Epic Question 5 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 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
Popular Question 7 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 8 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 8 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 11 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 11 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 11 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 13 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 17 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 17 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 18 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Popular Question 19 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot

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