User: banerjeeshayantan
banerjeeshayantan • 70
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Posts by banerjeeshayantan
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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 6 days ago by
banerjeeshayantan • 70
• updated
6 days ago by
Ram ♦ 17k
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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 6 days ago by
banerjeeshayantan • 70
• updated
6 days ago by
jared.andrews07 • 870
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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 9 days ago by
banerjeeshayantan • 70
• updated
9 days ago by
genomax ♦ 54k
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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
banerjeeshayantan • 70
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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 10 days ago by
banerjeeshayantan • 70
• updated
10 days ago by
h.mon ♦ 18k
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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 11 days ago by
banerjeeshayantan • 70
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212
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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
banerjeeshayantan • 70
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212
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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
banerjeeshayantan • 70
0
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212
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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
banerjeeshayantan • 70
0
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1
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212
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1
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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
banerjeeshayantan • 70
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