User: banerjeeshayantan

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Posts by banerjeeshayantan

<prev • 162 results • page 1 of 17 • next >
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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 6 days ago by banerjeeshayantan70 • updated 6 days ago by Ram17k
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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 6 days ago by banerjeeshayantan70 • updated 6 days ago by jared.andrews07870
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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 9 days ago by banerjeeshayantan70 • updated 9 days ago by genomax54k
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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 days 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 days ago by banerjeeshayantan70 • updated 10 days ago by h.mon18k
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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 11 days ago by banerjeeshayantan70
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Comment: C: VEP output has no gene names
... Hi again. The VEP 67 version link is down. Are you aware of any active links? ...
written 12 days ago by banerjeeshayantan70
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Comment: C: VEP output has no gene names
... Thanks for suggesting the steps. I will try it out. This really helped! Thanks again. ...
written 12 days ago by banerjeeshayantan70
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Comment: C: VEP output has no gene names
... Thanks for pointing it out. If possible, Can you please direct me to the appropriate link? ...
written 12 days ago by banerjeeshayantan70
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Comment: C: VEP output has no gene names
... I used the cache file from [this page][1] under the mouse genome and column known as "variation vep". This resulted in opening of a page from where I downloaded the mus_musculus_vep_93_GRCm38.tar.gz file.Did I do anything wrong? [1]: https://asia.ensembl.org/info/data/ftp/index.html ...
written 12 days ago by banerjeeshayantan70

Latest awards to banerjeeshayantan

Popular Question 28 days ago, created a question with more than 1,000 views. For Variant calling using samtools
Centurion 3 months ago, created 100 posts.
Supporter 4 months ago, voted at least 25 times.

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