User: vinayjrao

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vinayjrao110
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JNCASR, India
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3 months, 1 week ago
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Posts by vinayjrao

<prev • 106 results • page 1 of 11 • next >
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Comment: C: Is there a code to find consensus motif
... That's an extremely handy option. Thanks again :) ...
written 4 months ago by vinayjrao110
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Comment: C: Is there a code to find consensus motif
... Thanks. This works too. I could use the `.{2}` when I have larger repeats of any nucleotide/amino acid. Although, I would like to know why it `[\1G]` and not `[ATG]`? ...
written 4 months ago by vinayjrao110
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Comment: C: Is there a code to find consensus motif
... Thanks a lot. It's perfect. ...
written 4 months ago by vinayjrao110
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Is there a code to find consensus motif
... Hello, I've been trying to write a code to find a consensus motif in a given sequence, and for this purpose, I was only able to reach till finding a substring in a string. I want to be able to allot multiple nucleotides/amino acids at each position, and also enter N/X representing any of the nucleo ...
python C shell awk written 4 months ago by vinayjrao110 • updated 4 months ago by Carlo Yague4.3k
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Comment: C: Need help in GSEA analysis and interpretation
... I'm sorry for the incomplete information, I used the GSEA tool published by Broad Institute. The organism was human, and I was specifically looking into the HR Defect signature as described by Peng et al. The aim is study the enrichment of the geneset after tumor induction. I used the h.all referen ...
written 4 months ago by vinayjrao110
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Comment: C: Need help in GSEA analysis and interpretation
... It's actually only 10 genes represented in the barcode plot, but yes they belong to 10 different genesets. I'm sorry for the incomplete information, I used the GSEA tool published by Broad Institute. The organism was human, and I was specifically looking into the HR Defect signature as described by ...
written 4 months ago by vinayjrao110
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Need help in GSEA analysis and interpretation
... Hello, I am performing GSEA to study the enrichment of a particular geneset upon tumor induction. I have run the analysis using default parameters and the barcode plot generated only shows 10 significant genes enriched out of 215. I want to know if it could imply biological significance, or have I ...
barcode plot gsea rna-seq written 4 months ago by vinayjrao110
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Comment: C: Effect of splice site mutations in mouse
... Ankit, If you want to study the effects of the mutation at the protein level, you could translate and perform a BLAST. If sequences aren't reported, those would be novel variants. ...
written 5 months ago by vinayjrao110
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Comment: C: Effect of splice site mutations in mouse
... Ankit, At what level do you want to understand the effect of the mutations? If it's at the protein level, you could simply translate your sequences and perform a BLAST. In cases where you get a high query cover and identity would carry mutations in regions other than the splice sites. In case of sp ...
written 5 months ago by vinayjrao110
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Comment: C: Effect of splice site mutations in mouse
... If you have a set of canonical splice variants of each gene, then you could separate out only the non-canonical variants and look for the mutations. Once you find the mutations, you could check if the variant and its effects have been reported. ...
written 5 months ago by vinayjrao110

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Popular Question 5 months ago, created a question with more than 1,000 views. For understanding bedtools coverage output
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