User: Chirag Nepal

gravatar for Chirag Nepal
Chirag Nepal2.0k
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ChiragNepal
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Posts by Chirag Nepal

<prev • 285 results • page 1 of 29 • next >
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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 1 day 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 1 day 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 1 day 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 4 days 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 days ago by Chirag Nepal2.0k
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Mapping variable read length
... Hi There, Does anyone have a recommendation on tools that allow to map reads of variable length (between 18-300 nt) as can be seen here https://www.dropbox.com/s/10dn098492zst9i/Length.png?dl=0 I had previously (6 years back) used blat to map such cases, and use percent identity to get mapped r ...
alignment written 10 days ago by Chirag Nepal2.0k
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Comment: C: about somatic mutation calling
... Yes, that is nice. I have two questions. Among the called somatic variants, variants are classified as PASS(high confident) and into Tier1 to Tier5. What do you think is reasonable to include for downstream filtering. This is the total count i had in my cohort of around 100 patients PASS 17846 ...
written 13 days ago by Chirag Nepal2.0k
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Comment: C: about somatic mutation calling
... Yes, please. I removed the commented lines. Here are the first 5 lines of called somatic variants > > **#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL** > > chr1 1274696 . G T . Tier5 SOMATIC GT:DP:AD:BQ:SS 0/1:42:39,3:35,37:2 0/0:15:15,0:36,0:. > > chr1 2451820 . C ...
written 14 days ago by Chirag Nepal2.0k
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Comment: C: about somatic mutation calling
... Thanks Bogdan ! I did use similar command, as mentioned previously in the above link. However, i get error. I tried MuSE. It works fine. ...
written 15 days ago by Chirag Nepal2.0k
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Comment: C: about somatic mutation calling
... Thank you !! Looking forward for your reply in the above post. I have already used Mutect and Varscan. I wanted to try Virmid, but have not been successful in running it. ...
written 17 days ago by Chirag Nepal2.0k

Latest awards to Chirag Nepal

Good Answer 6 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
Student 10 weeks 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 11 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 3 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 5 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 8 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 8 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 9 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Popular Question 10 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Popular Question 11 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Great Question 13 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 14 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 14 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
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?
Great Question 21 months ago, created a question with more than 5,000 views. For Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
Great Question 22 months ago, created a question with more than 5,000 views. For GATK, SAM file doesn't have any read groups defined in the header

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