User: banerjeeshayantan

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Posts by banerjeeshayantan

<prev • 166 results • page 1 of 17 • next >
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What is the significance of this file in COSMIC database?
... I was going through the [COSMIC database ][1]and came across a particular file in the downloads page. This file was named Fasta file (genes) and its description was "CDS sequence for all the genes in COSMIC". Now I understand that these are the fasta sequences of all the genes listed in the COSMIC d ...
genome next-gen snp written 3 months ago by banerjeeshayantan70
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Mice driver mutations
... I have 10 normal-tumor paired genomes of mice suffering from pancreatic cancer. I have started doing the usual NGS analysis of checking the quality of bam reads, calling variants and annotating them. Now I want to find driver mutations and subsequently driver genes from the samples. Now, most of the ...
mice genome driver mutaions written 3 months ago by banerjeeshayantan70 • updated 3 months ago by sophiespo90
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Comment: C: Flanking sequences around cancer variants
... thanks for your comment. It makes sense to build a consensus sequence and extract the flanking sequence. We should take steps to ensure that cancerous variants are not included in the flanking sequences. For the variation question, I will reply to this thread if I have more information. ...
written 3 months ago by banerjeeshayantan70
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Flanking sequences around cancer variants
... I want to analyze the flanking sequences around cancer variants. I have already downloaded cancer variants from COSMIC database. Now I am planning to extract variants from the reference build of the variant database (hg38 in this case) using bioMart. But I am having doubts regarding whether the flan ...
genome cancer_variants snp written 3 months ago by banerjeeshayantan70 • updated 3 months ago by jared.andrews071.7k
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MuSiC2 bmr calculation
... I am trying to calculate background mutation rate to find some genes of interest. I am using MuSiC2 for the job using the following command ... music bmr calc-bmr \ --bam-list input_dir/bam_list \ --maf-file input_dir/myMAF.tsv \ --output-dir output_dir/ \ --reference-sequence ...
music2 sequencing written 4 months ago by banerjeeshayantan70 • updated 4 months ago by RamRS19k
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Which are the regulatory regions among the following?
... Being from a non-bio background I am finding it hard to discover which among the following are regulatory regions and coding regions. I am interested in finding variants in regulatory regions of the genome. I have a maf file with all the regions mapped out. [1] "3_prime_UTR_variant" ...
assembly sequencing written 4 months ago by banerjeeshayantan70 • updated 4 months ago by jared.andrews071.7k
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Error downloading MuSiC2
... I am following all the steps that are required to install music2. I am trying to download calcRoiCovg in one of the steps. I have followed all the instructions previously, but I am getting the following error. gcc -g -Wall -fopenmp -O2 -Idata/shayantan/samtools/ calcRoiCovg.c -o calcRoiCov ...
software error ngs music2 sequencing written 4 months ago by banerjeeshayantan70 • updated 4 months ago by genomax59k
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Comment: C: Problems downloading MuSiC
... Can I use [this][1] instead? Its MuSic2. [1]: https://github.com/ding-lab/MuSiC2 ...
written 4 months ago by banerjeeshayantan70
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Problems downloading MuSiC
... I am trying to download MuSiC from the Genome Institute at Washington University School of Medicine [link][1] But the site is unresponsive for almost a day now. It's taking forever to connect. Any suggestions? I am ready to use any driver mutation prioritization tools as long as it works on paired m ...
software error music written 4 months ago by banerjeeshayantan70 • updated 4 months ago by h.mon21k
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Identifying driver mutations in mice cancer data
... I have 10 normal-tumor samples containing mice PDAC data. I have already called variants and annotated them. Now I wanted to use conventional driver mutation tools to identify recurrently mutated variants in each of the samples. I was planning to use MutSigCV, but they are mostly used for the human ...
genome assembly snp sequencing written 4 months ago by banerjeeshayantan70

Latest awards to banerjeeshayantan

Popular Question 4 months ago, created a question with more than 1,000 views. For Variant calling using samtools
Centurion 7 months ago, created 100 posts.
Supporter 8 months ago, voted at least 25 times.

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