User: Chirag Nepal
Chirag Nepal • 2.2k
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- ChiragNepal
- Last seen:
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- Joined:
- 8 years, 11 months ago
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Posts by Chirag Nepal
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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 7 months ago by
Chirag Nepal • 2.2k
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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 7 months ago by
Chirag Nepal • 2.2k
• updated
7 months ago by
Pierre Lindenbaum ♦ 131k
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... Thank you !! I wanted to confirm. ...
written 7 months ago by
Chirag Nepal • 2.2k
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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 7 months ago by
Chirag Nepal • 2.2k
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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 Nepal • 2.2k
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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 8 months ago by
Chirag Nepal • 2.2k
• updated
8 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 16 months ago by
Chirag Nepal • 2.2k
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25k
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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 21 months ago by
Chirag Nepal • 2.2k
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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 23 months ago by
Chirag Nepal • 2.2k
1
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... 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. ...
written 2.4 years ago by
Chirag Nepal • 2.2k
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For Transcriptional regulator genes list
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
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For Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
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For Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
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For C: Extract rows from BED file on the base of text content in one column
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
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For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
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For A: help with career decisions: should a PhD in genetics go for another master in bi
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For Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
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For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
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For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
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For GATK, SAM file doesn't have any read groups defined in the header
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For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
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