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 5 weeks 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 6 weeks ago by banerjeeshayantan70 • updated 6 weeks ago by sophiespo60
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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 6 weeks 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 6 weeks ago by banerjeeshayantan70 • updated 6 weeks ago by jared.andrews071.3k
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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 9 weeks ago by banerjeeshayantan70 • updated 9 weeks ago by RamRS18k
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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 9 weeks ago by banerjeeshayantan70 • updated 9 weeks ago by jared.andrews071.3k
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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 10 weeks ago by banerjeeshayantan70 • updated 10 weeks ago by genomax57k
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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 10 weeks 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 10 weeks ago by banerjeeshayantan70 • updated 10 weeks ago by h.mon20k
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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 10 weeks ago by banerjeeshayantan70

Latest awards to banerjeeshayantan

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Variant calling using samtools
Centurion 5 months ago, created 100 posts.
Supporter 6 months ago, voted at least 25 times.

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