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:
15 hours ago
Joined:
8 years, 11 months ago
Email:
n*************@gmail.com

Posts by Chirag Nepal

<prev • 304 results • page 1 of 31 • next >
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Comment: C: Find HBV integration sites in human genome.
... Thank you Pierre ! So you suggest to merge genome sequence of human + virus. Then map the unmapped reads using BWA on combined genome assembly. Reads that map partially to human and virus will be flagged as discordant. I think it is a neat idea. What is the flag for discordant reads. ...
written 7 months ago by Chirag Nepal2.2k
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Find HBV integration sites in human genome.
... Hi there, I want to identify HBV (virus) integration sites in human genome. I have single end CAGE-seq (~30 nucleotide long) data on HBV patients. I mapped reads to human genome (used Bowtie2 version 2.29), and unmapped reads were mapped to HBV genome. From the remaining unmapped reads, I want t ...
chimericreads humanvirusgenome cage-seq written 7 months ago by Chirag Nepal2.2k • updated 7 months ago by Pierre Lindenbaum131k
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Comment: C: Mapping reads on ENCODEBlackListedRegion
... Thank you !! I wanted to confirm. ...
written 7 months ago by Chirag Nepal2.2k
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Mapping reads on ENCODEBlackListedRegion
... Hi there, A lot of CAGE tags map to the encode blacklisted region. I have only mapped the unique reads. I exclude these ~600 regions from downstream analysis. Do you think it is good idea to excluded them at the mapping step. Or is it good to exclude after mapping, so that normalization of tags (to ...
encodeblacklistedregion cage-seq written 7 months ago by Chirag Nepal2.2k
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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 8 months 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 8 months ago by Chirag Nepal2.2k • updated 8 months ago by jbalberge150
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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 16 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 21 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 23 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 2.4 years ago by Chirag Nepal2.2k

Latest awards to Chirag Nepal

Popular Question 25 days ago, created a question with more than 1,000 views. For Transcriptional regulator genes list
Great Question 12 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.
Epic Question 12 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.
Scholar 12 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
Great Question 2.0 years 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 2.3 years 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 2.4 years 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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