User: Chirag Nepal

gravatar for Chirag Nepal
Chirag Nepal2.2k
Reputation:
2,250
Status:
Trusted
Location:
Copenhagen
Website:
http://scholar.google....
Twitter:
ChiragNepal
Last seen:
3 days, 17 hours ago
Joined:
8 years, 3 months ago
Email:
n*************@gmail.com

Posts by Chirag Nepal

<prev • 300 results • page 1 of 30 • next >
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Comment: C: Visualize paired end reads
... Hi Pierre, I added the twitter url to show the image of what i was describing. In that case, i will now remove the twitter url from here. Not gonna do that again. thanks ! ...
written 7 days ago by Chirag Nepal2.2k
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Visualize paired end reads
... Hi There Any suggestion on how to visualize the connection between two reads/fragments of paired end RNA-seq data. The screenshot of the description is posted here One paired ends are map to the genome by using BLAT (shown on top as black bar). Aligned reads from STAR are shown in blue and red. T ...
paired-end alignment rna-seq written 7 days ago by Chirag Nepal2.2k • updated 3 days ago by jbalberge100
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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 8 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 13 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 15 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 20 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 20 months ago by Chirag Nepal2.2k • updated 20 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 21 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 22 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 22 months ago by Chirag Nepal2.2k

Latest awards to Chirag Nepal

Scholar 3 months ago, created an answer that has been accepted. For C: Extract rows from BED file on the base of text content in one column
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.
Great Question 16 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 19 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 20 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.

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