User: elvissober

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elvissober20
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20
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Location:
South Africa
Last seen:
5 years, 1 month ago
Joined:
5 years, 1 month ago
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Programmer

Posts by elvissober

<prev • 21 results • page 1 of 3 • next >
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(Closed) How to do batch processing with mpileup in a Linux shell for loop?
... want to make VCFs on a set of .sams (.bams): for i in ls (*.sam)                  # calling variants on .sam files do          ./samtools mpileup -R -d | bcftools view -g - > test.vcf $i    # what to write here correctly? done   ...
samtools shell bash written 5.1 years ago by elvissober20
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(Closed) How to run BBMap in a Lubux shell for loop?
... for i in ls (*.fastaq)                  #  mapping fastq files to a preset reference do          ./bbmap.sh $i                  done   How to pass arguments after .sh call, what to write? ...
sequencing bbmap shell bash written 5.1 years ago by elvissober20
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Comment: C: How to pass shell script`s arguments when calling BBMap from Python?
... what arguments to pass to subprocess.call()? thx ...
written 5.1 years ago by elvissober20
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How to use Ruby BioSamtools for SNP finding on .bam and .sam files?
... How to use Ruby BioSamtools for SNP finding on .bam and .sam files? Does my code call variants or not, I am not sure... #!/usr/bin/ruby # making script executable require 'bio-samtools' # calling rubygem bam=Bio::DB::Sam.new(:bam=>"my.bam",:fasta=>'fake.fa') # creating bam object bam.open b ...
ruby bioruby samtools written 5.1 years ago by elvissober20 • updated 4.6 years ago by Biostar ♦♦ 20
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How to pass shell script`s arguments when calling BBMap from Python?
... How to pass shell script`s arguments when calling BBMap from Python? Trying to call BBMap from Python 2.7. There are subprocess and os modules for that. All efforts are wrong. Here is a code: import os import subprocess os.chdir(r"/home/user/Documents/bbmap") # changing the directory to run subs ...
python sequencing soft shell bash written 5.1 years ago by elvissober20
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Answer: A: UCSC browser gives two sets of exons for a Refseq ID (f and r) - SNP interpretat
... Try Ugene browser, that is the only thing what is good there, you know... ...
written 5.1 years ago by elvissober20 • updated 13 months ago by _r_am32k
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Comment: C: How to do variant calling on .sam and .bam files using 'bio-samtools'?
... Need all in one Ruby workflow, thank you for you replies ...
written 5.1 years ago by elvissober20
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Comment: C: How to run a batch .sra to .fastq processing loop using linux bash?
... Thank you, folks, how clever you are!!! ...
written 5.1 years ago by elvissober20
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What R packages and functions can perform variant calling on .sam and .bam files?
... What R packages and their functions can perform variant calling on .sam and .bam files? Need a commented clear code example. Found RSamtools. No concrete examples in their documentation therein. ...
sequencing wgs sequence R written 5.1 years ago by elvissober20 • updated 5.0 years ago by Michael Dondrup48k
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How to do variant calling on .sam and .bam files using 'bio-samtools'?
... How to  do variant calling on .sam files using 'bio-samtools'? I have the code; #!/usr/bin/ruby require 'bio-samtools' bam = Bio::DB::Sam.new(:bam=>"my_sorted.bam", :fasta=>'ref.fasta')   bam.open   What methods to call on bam object or what next steps to do? Thank you.   ...
software error wgs sequence sequencing written 5.1 years ago by elvissober20 • updated 5.1 years ago by Sean Davis26k

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