User: Chirag Nepal

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Chirag Nepal1.9k
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ChiragNepal
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4 hours ago
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Posts by Chirag Nepal

<prev • 273 results • page 1 of 28 • next >
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Comment: C: Excised exon or transcribed snoRNA?
... Can you show a browser screenshot for any gene ? If you think it is snorna, you can probably check iCLIP data for snoRNP complex, i think it was paper in genome biology. **Update:** Honestly, not sure, what is going on there. However i would check few things 1) Is this one of the case, or there ar ...
written 10 days ago by Chirag Nepal1.9k
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Comment: C: Uniquely mapped in Human
... Do quality checking of your reads by using fastqc. If there is rRNA, throw them out before mapping. Is this data 101*2 pair end reads or 202 bp single end read. ...
written 8 weeks ago by Chirag Nepal1.9k
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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 3 months 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 3 months 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 3 months ago by Chirag Nepal1.9k • updated 3 months 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 4 months 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 6 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 6 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 7 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 7 months ago by Chirag Nepal1.9k

Latest awards to Chirag Nepal

Epic Question 8 weeks 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 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)
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)
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Popular Question 7 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Popular Question 8 months ago, created a question with more than 1,000 views. For How To Smooth Ecdf Plot
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Great Question 10 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 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?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Scholar 13 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 18 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 19 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 19 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 19 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How to find CpG island shore?

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