User: Chirag Nepal

gravatar for Chirag Nepal
Chirag Nepal1.9k
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Copenhagen
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ChiragNepal
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5 hours ago
Joined:
5 years, 10 months ago
Email:
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Posts by Chirag Nepal

<prev • 271 results • page 1 of 28 • next >
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Comment: C: Virus sequence detected in my RNA-seq reads
... You could try to make the situation work in your favor. Try to see how those patients/cell-lines with virus and different from rest of samples in transcriptomics profile. ...
written 27 days ago by Chirag Nepal1.9k
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Comment: C: miRNA identification from RNA seq data
... Which protocol did you use for library preparation ? Unless you have enriched for small RNAs (by size selection of your interest, mostly 18-30 nucleotides ), most RNA-seq data is unlikely to capture miRNAs. RNA-seq data might be 70-100 bases long, even after excluding primers/adapter, much longer th ...
written 7 weeks ago by Chirag Nepal1.9k
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Transcriptional strand bias on SNV from exome data
... Hi there, I want to find SNV that show bias in transcribed/untranscribed strand Here is one SNV from varscan, with tumor/normal read counts, with header and data chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1 tumor_reads2 tumor_var_freq tumor_gt soma ...
exome strand-bias snv written 7 weeks ago by Chirag Nepal1.9k • updated 4 weeks ago by Biostar ♦♦ 20
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Comment: C: What is the recommended sequencing depth for ChIRP-seq?
... In my opinion, 100M should be very good. You could check ChRiP papers and see what was their sequencing depth. ...
written 8 weeks ago by Chirag Nepal1.9k
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Comment: C: Plotting copy number varation: amplification and deletion data from GISTIC
... I used GISTIC2 and used the figure from it. I added gene names using illustrator. ...
written 4 months ago by Chirag Nepal1.9k
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Comment: C: How to get promoter coordinates of hg19 from UCSC genome browser ?
... There was one closing bracket missing, edited it, try it now. ...
written 4 months ago by Chirag Nepal1.9k
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Comment: C: Mismatch on first base gives wrong TSS
... Thanks Charles !!! I also think post-processing BAM file might be better solution, basically if there is a mismatch of "G" on first base, exclude that base and shift TSS. ...
written 5 months ago by Chirag Nepal1.9k
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Comment: C: trimming reads in fastq file
... That tool seems nice !! Charles, i have a slightly related question, regarding triming of first base. I was looking at modEncode CAGE data, and i see there is a very high percentage of first base added on Fastq sequence, but not on all sequence. First base is generallt "G" as it is known. I mapped ...
written 5 months ago by Chirag Nepal1.9k
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Comment: C: Displaying somatic mutational signatures
... Does SomaticSignature package tells whether the identified signature is similar to signature-1 or signature-2 ........signature-30 from http://cancer.sanger.ac.uk/cosmic/signatures I did not find in the manual where it said how similar it is to cosmic signatures. ...
written 6 months ago by Chirag Nepal1.9k
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Comment: C: Mismatch on first base gives wrong TSS
... Reference nucleotide at 1450199 is also C. The insertion of "G" at first base is known bias of CAGE (though it does not occur in all reads), and it is filtered out to get correct information about TSS. It seems modEncode did not correct this. TSS (CTTTCCGG), is perfectly valid. The first nucleoti ...
written 7 months ago by Chirag Nepal1.9k

Latest awards to Chirag Nepal

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)
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)
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Popular Question 5 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Popular Question 6 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Scholar 9 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 9 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Scholar 11 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 11 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
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.
Great Question 17 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
Good Answer 17 months 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
Teacher 17 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 17 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Librarian 18 months ago, created a post with more than 10 bookmarks. For Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.

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