User: banerjeeshayantan

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Posts by banerjeeshayantan

<prev • 183 results • page 1 of 19 • next >
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Strand information for cancer variants from COSMIC
... I have a very basic question. So I have downloaded somatic mutation data from the COSMIC database. Each mutation has corresponding strand information associated with them. This usually coincides with the coding strand of the gene in which the mutation is located. The strand information goes like "+" ...
genome cosmic snp written 11 days ago by banerjeeshayantan80
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Comment: C: strand-biased mutation analysis on WES data
... So if I want to extract fasta sequence of the flanking regions around mutations (SNVs), I should just consider all the mutations to be in one particular strand and go ahead with the analysis (bedtools getfasta), right? ...
written 11 days ago by banerjeeshayantan80
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Comment: C: Significance of motifs around mutations
... Thanks for your reply. I have tried something very similar to your first suggestion. I tried finding motifs that are over-represented around disease-causing mutations as compared to non-disease. I also have a list of such motifs with their respective significance values. But the problem is I am unab ...
written 15 days ago by banerjeeshayantan80
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Comment: C: Over- or under-represented motifs in coding regions
... I have a list of mutations and the motifs are the bases flanking the mutation. I want to check whether over-representation of certain motifs influences the type of mutation. ...
written 21 days ago by banerjeeshayantan80
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Over- or under-represented motifs in coding regions
... I have a set of di-, tri- and tetra-nucleotide motifs from the coding region of the genome that are over-represented. Is there any way to establish the biological significance of the over-representation? Right now it's just statistically significant with respect to a null model (of random sequences ...
R snp written 21 days ago by banerjeeshayantan80
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Comment: C: Regular expression to extract mutations type
... Sorry about that. I have read the link you shared and will definitely consider them all while asking questions in the future. ...
written 22 days ago by banerjeeshayantan80
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Comment: C: Regular expression to extract mutations type
... Apologies for not being clear. There can be other mutation types also like G>T, G>C,T>A... etc. ...
written 22 days ago by banerjeeshayantan80
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Regular expression to extract mutations type
... I have a list of strings of the format `"c.2455C>T"`. How can I extract the mutation type or the `"C>T"` part from the string? ...
R regex written 22 days ago by banerjeeshayantan80 • updated 22 days ago by manuel.belmadani450
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Comment: C: Randomly sample motifs from reference sequence
... Hi, This is a great tool. thanks a lot for suggesting. Can you also specify how not to get Ns in my results? How do I mask that? Removing mask=NA from the above code isn't helping. ...
written 23 days ago by banerjeeshayantan80
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Comment: C: Randomly sample motifs from reference sequence
... Say there are 2899452029 base pairs in the reference genome. Then I can choose the starting position of the kmer uniformly from 1 to 2899452029 at random. This will continue until I get the required number of kmers. ...
written 24 days ago by banerjeeshayantan80

Latest awards to banerjeeshayantan

Popular Question 22 days ago, created a question with more than 1,000 views. For Samtools flagstat results
Popular Question 4 months ago, created a question with more than 1,000 views. For Checking bam quality
Popular Question 4 months ago, created a question with more than 1,000 views. For When can I distinguish between an SNV and a sequencing error?
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