User: Chirag Nepal
Chirag Nepal • 2.3k
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- ChiragNepal
- Last seen:
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- Joined:
- 9 years, 3 months ago
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Posts by Chirag Nepal
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... Interesting idea. I plan to analyze this, not sure what it might (potentially reflects heterogeneity) mean. Would you minding sharing your insight from your analysis or refer to your paper if it is already published. ...
written 3 months ago by
Chirag Nepal • 2.3k
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... 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 11 months ago by
Chirag Nepal • 2.3k
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... 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 ...
written 11 months ago by
Chirag Nepal • 2.3k
• updated
11 months ago by
Pierre Lindenbaum ♦ 134k
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... Thank you !! I wanted to confirm. ...
written 11 months ago by
Chirag Nepal • 2.3k
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... 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 ...
written 11 months ago by
Chirag Nepal • 2.3k
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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 12 months ago by
Chirag Nepal • 2.3k
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... 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 ...
written 12 months ago by
Chirag Nepal • 2.3k
• updated
12 months ago by
jbalberge • 150
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... If you could attach a screenshot with coverage tracks, it becomes easier and meaningful to interpret the signal.
...
written 20 months ago by
Chirag Nepal • 2.3k
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... 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 2.1 years ago by
Chirag Nepal • 2.3k
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... 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 2.3 years ago by
Chirag Nepal • 2.3k
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