User: Chirag Nepal

gravatar for Chirag Nepal
Chirag Nepal2.2k
Reputation:
2,230
Status:
Trusted
Location:
Copenhagen
Website:
http://scholar.google....
Twitter:
ChiragNepal
Last seen:
2 weeks, 1 day ago
Joined:
8 years ago
Email:
n*************@gmail.com

Posts by Chirag Nepal

<prev • 298 results • page 1 of 30 • next >
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Comment: C: Can we combine adjacent peaks in ATAC-Seq fata
... If you could attach a screenshot with coverage tracks, it becomes easier and meaningful to interpret the signal. ...
written 5 months ago by Chirag Nepal2.2k
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Comment: C: Drug to Target/Gene/Protein Interaction Databases
... 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 9 months ago by Chirag Nepal2.2k
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Comment: C: Identifying pri-microRNA sequence from microRNA sequence
... 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 12 months ago by Chirag Nepal2.2k
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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 17 months ago by Chirag Nepal2.2k
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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 17 months ago by Chirag Nepal2.2k • updated 17 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 18 months ago by Chirag Nepal2.2k
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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 19 months ago by Chirag Nepal2.2k
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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 19 months ago by Chirag Nepal2.2k
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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 19 months ago by Chirag Nepal2.2k
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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 19 months ago by Chirag Nepal2.2k • updated 19 months ago by d-cameron2.1k

Latest awards to Chirag Nepal

Great Question 13 months ago, created a question with more than 5,000 views. For Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
Good Question 16 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 17 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 19 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 20 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 20 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 21 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

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