User: Chirag Nepal

gravatar for Chirag Nepal
Chirag Nepal2.0k
Reputation:
2,020
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Location:
Copenhagen
Website:
http://scholar.google....
Twitter:
ChiragNepal
Last seen:
3 hours ago
Joined:
6 years, 5 months ago
Email:
n*************@gmail.com

Posts by Chirag Nepal

<prev • 290 results • page 1 of 29 • next >
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Comment: C: Tophat2 error: failed to retrieve right/left read for pair
... https://twitter.com/lpachter/status/937055346987712512 Why don't you use other better/fast tools like STAR, HiSAT, kallisto and others. ...
written 6 days ago by Chirag Nepal2.0k
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Count intron retention reads from BAM files
... Hi there, How to find/filter intron-retained reads from BAM files? Which flag in BAM file describes information about retained intron. I know there are some tools to find retained intron, but i want to understand how they are represented in BAM files. When there is an intron retention, portion of ...
intron-retention samtools written 21 days ago by Chirag Nepal2.0k • updated 21 days ago by d-cameron1.5k
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Comment: A: Tophat not installing with Biostar Handbook
... Authors of Tophat paper recommend not to use the software anymore. https://twitter.com/lpachter/status/937055346987712512 ...
written 26 days ago by Chirag Nepal2.0k
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Comment: C: How to determine high-quality somatic mutations
... varscan2, somaticSnipper, virmid, strelka and many more. ...
written 5 weeks ago by Chirag Nepal2.0k
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Comment: C: Finding zebrafish promoters ENSEMBL
... Promoter region is kinda arbitrarily defined somewhere between 2/300 bases to 2000 bases upstream of annotated TSS (transcription start sites) from Ensembl/Refseq. So you can extract 2KB region upstream of TSS and get promoter region. CAGE-seq is best way to define TSS, and have a look at this paper ...
written 7 weeks ago by Chirag Nepal2.0k
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Comment: C: Small RNA sequence, how to calculate read counts? What's the criterion? Is there
... Thanks Sean !! I did it here https://www.biostars.org/p/300146/ ...
written 8 weeks ago by Chirag Nepal2.0k
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Comment: C: Best/right way to quantify small RNA transcripts
... Thanks Igor !! I updated in the above post to clarify further. This is not a typical miRNA-seq data which is enriched for 18-30 nt RNAs. Mapping is fine with bowtie2, get around 85-90% of mapping. The only concern i am having is regarding normalization when **converting reads_counts into reads_per ...
written 8 weeks ago by Chirag Nepal2.0k
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Best/right way to quantify small RNA transcripts
... Hi there, I want to quantify read counts of small RNAs into reads per million (RPM). Which is the correct/best way to do ? small RNAs map to multiple locations in the genome. Here is the plot to show length of sequence reads, which are of variable length. https://www.dropbox.com/s/10dn098492zst9 ...
multi-mapping rpm small rna-seq written 8 weeks ago by Chirag Nepal2.0k
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Comment: C: Small RNA sequence, how to calculate read counts? What's the criterion? Is there
... When converting read counts of small RNA into reads per million (RPM), how to define "Total_number_mapped_reads". **For example, in one of the mapped small RNA library** > 2601833 reads; of these: 2601833 (100.00%) were unpaired; of these: > 352919 (13.56%) aligned 0 times > ...
written 9 weeks ago by Chirag Nepal2.0k
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Comment: C: about somatic mutation calling
... PASS is the most stringent called variants. For WES, it is recommended that Tier-5 can be excluded for WES, but also suggested to compare with other tools, as that might decrease false positive. Other thing is, muse reports LOH as somatic events, while varscan2 separates LOH from somatic events. ...
written 10 weeks ago by Chirag Nepal2.0k

Latest awards to Chirag Nepal

Good Answer 7 days ago, created an answer that was upvoted at least 5 times. For A: help with career decisions: should a PhD in genetics go for another master in bi
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: help with career decisions: should a PhD in genetics go for another master in bi
Student 4 months ago, asked a question with at least 3 up-votes. For GATK, SAM file doesn't have any read groups defined in the header
Popular Question 4 months ago, created a question with more than 1,000 views. For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Popular Question 5 months ago, created a question with more than 1,000 views. For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Epic Question 7 months ago, created a question with more than 10,000 views. For GATK, SAM file doesn't have any read groups defined in the header
Popular Question 10 months ago, created a question with more than 1,000 views. For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Popular Question 10 months ago, created a question with more than 1,000 views. For Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Popular Question 12 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Popular Question 13 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Great Question 15 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.
Scholar 16 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
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Scholar 18 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 23 months ago, created a question with more than 5,000 views. For Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.

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