User: Chirag Nepal
Chirag Nepal • 2.0k
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Posts by Chirag Nepal
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... 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 Nepal • 2.0k
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67
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... 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 ...
written 21 days ago by
Chirag Nepal • 2.0k
• updated
21 days ago by
d-cameron • 1.5k
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1
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... Authors of Tophat paper recommend not to use the software anymore.
https://twitter.com/lpachter/status/937055346987712512
...
written 26 days ago by
Chirag Nepal • 2.0k
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110
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... varscan2, somaticSnipper, virmid, strelka and many more. ...
written 5 weeks ago by
Chirag Nepal • 2.0k
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... 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 Nepal • 2.0k
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... Thanks Sean !! I did it here https://www.biostars.org/p/300146/ ...
written 8 weeks ago by
Chirag Nepal • 2.0k
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... 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 Nepal • 2.0k
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200
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... 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 ...
written 8 weeks ago by
Chirag Nepal • 2.0k
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... 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 Nepal • 2.0k
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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 Nepal • 2.0k
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For GATK, SAM file doesn't have any read groups defined in the header
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