User: banerjeeshayantan
banerjeeshayantan • 70
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Posts by banerjeeshayantan
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2
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... 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 ...
written 3 months ago by
banerjeeshayantan • 70
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1
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... 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 ...
written 3 months ago by
banerjeeshayantan • 70
• updated
3 months ago by
sophiespo • 90
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... 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
banerjeeshayantan • 70
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... 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 ...
written 3 months ago by
banerjeeshayantan • 70
• updated
3 months ago by
jared.andrews07 • 1.7k
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229
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... 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 ...
written 4 months ago by
banerjeeshayantan • 70
• updated
4 months ago by
RamRS ♦ 19k
2
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1
answer
209
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1
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... 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" ...
written 4 months ago by
banerjeeshayantan • 70
• updated
4 months ago by
jared.andrews07 • 1.7k
0
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1
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172
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1
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... 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 ...
written 4 months ago by
banerjeeshayantan • 70
• updated
4 months ago by
genomax ♦ 59k
0
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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
banerjeeshayantan • 70
2
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0
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218
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... 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 ...
written 4 months ago by
banerjeeshayantan • 70
• updated
4 months ago by
h.mon ♦ 21k
0
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0
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179
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... 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 ...
written 4 months ago by
banerjeeshayantan • 70
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