User: Chirag Nepal
Chirag Nepal • 2.2k
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- Joined:
- 8 years, 3 months ago
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Posts by Chirag Nepal
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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 Nepal • 2.2k
1
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2
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95
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2
answers
... 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 7 days ago by
Chirag Nepal • 2.2k
• updated
3 days ago by
jbalberge • 100
1
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3
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561
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... If you could attach a screenshot with coverage tracks, it becomes easier and meaningful to interpret the signal.
...
written 8 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 13 months ago by
Chirag Nepal • 2.2k
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412
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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 15 months ago by
Chirag Nepal • 2.2k
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566
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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 20 months ago by
Chirag Nepal • 2.2k
0
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2
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813
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2
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... 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 ...
written 20 months ago by
Chirag Nepal • 2.2k
• updated
20 months ago by
lvulliard • 60
0
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3
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898
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3
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... You can use "**bedtools groupby**" command.
Show some example files, will behelpfulr to get precise answer. ...
written 21 months ago by
Chirag Nepal • 2.2k
0
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389
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... The authors of Tophat suggest not to use it, but Instead use Kallisto. Nice tutorials. ...
written 22 months ago by
Chirag Nepal • 2.2k
0
votes
1
answer
12k
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1
answers
... 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 Nepal • 2.2k
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
Popular Question
3 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Great Question
3 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
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.
Popular Question
3 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
9 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
10 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
13 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
14 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
14 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
14 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
15 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Appreciated
16 months ago,
created a post with more than 5 votes.
For A: help with career decisions: should a PhD in genetics go for another master in bi
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.
Popular Question
16 months ago,
created a question with more than 1,000 views.
For High throughput sequencing (RNA-seq, Chip-seq, CAGE-seq) coverage tracks from multiple species available for viewing on UCSC?
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
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
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19 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
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.
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
Appreciated
21 months ago,
created a post with more than 5 votes.
For A: help with career decisions: should a PhD in genetics go for another master in bi
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
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