User: elvissober

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elvissober20
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Location:
South Africa
Last seen:
4 years, 11 months ago
Joined:
4 years, 11 months ago
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Programmer

Posts by elvissober

<prev • 21 results • page 2 of 3 • next >
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What software produces VCF files from the .sam input?
... What software produces VCF files from the .sam input? SAMTools or there are some alternatives? ...
wgs sequence soft sequencing written 5.0 years ago by elvissober20 • updated 5.0 years ago by Pierre Lindenbaum131k
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How to install Picard/Pilons software and do variant call on a set of .sam files?
... How to install Picard software and do variant call on a set of .sam files? I have unzipped the archive, read the docs, not clear how to run it from a folder and what commands call variants on .sam and .bam files. Thank you. ...
software error wgs sequencing written 5.0 years ago by elvissober20 • updated 4.5 years ago by smkopac10
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Comment: C: Is it possible to include BBMap in Bcbio-nextgen pipeline?
... Need a clear tutorial on how to add tuberculosis microbe to that software and how to run a pipeline to process from a set of .sra files to .vcf and .pdf reports, thx ...
written 5.0 years ago by elvissober20
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How to run VCFTools and other variant callers on a set of .sam output of BBMap and other aligners?
... How to run VCFTools and other variant callers on .sam outputs of BBMap and other aligners? Need a clear example in Unix shell and from Python subprocess and Java/Ruby, please. Thank you. ...
vcf wgs sam soft sequencing written 5.0 years ago by elvissober20
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(Closed) How to run BBMap and VCFtools for a 200 of WGS .fasta files in a for loop in Shell or Bash without printing file names??
... How to run BBMap and VCFtools for a 200 of WGS .fasta files in a for loop in Shell or Bash without printing file names?? Have been advised to use that code for BBMap: bbmap.sh ref=ref.fa (wait for that to finish) bbmap.sh in=reads1.fq out=mapped1.sam bbmap.sh in=reads2.fq out=mapped2.sam bbmap.sh ...
wgs sequence sequencing written 5.0 years ago by elvissober20
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Comment: C: How to do BBmap batch processing correctly?
... Is there any possibility for a more prorgrammatic elegant way without rewriting file names and using for loops in Shell or Bash for that? Thank you. ...
written 5.0 years ago by elvissober20 • updated 11 months ago by _r_am31k
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Comment: C: How to do BBmap batch processing correctly?
... multiple sets of reads against one reference, thx ...
written 5.0 years ago by elvissober20 • updated 11 months ago by _r_am31k
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Comment: C: Is it possible to include BBMap in Bcbio-nextgen pipeline?
... I just have tried it and it does the job of producing .sam. However could not find a better software than Nextgen. Does anybody has a clear tutorial on using that ncbio for wgs from .sra to vcf? Thx. ...
written 5.0 years ago by elvissober20 • updated 11 months ago by _r_am31k
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Comment: C: Sambamba: High Performance Alternative For Samtools And Picard For Indexing, Sor
... How to install and use it correctly? I have: user@user-MS-7817:~/Documents/sambamba/sambamba$ make sambamba-ldmd2-64 make: *** No rule to make target `sambamba-ldmd2-64'. Stop. user@user-MS-7817:~/Documents/sambamba/sambamba$ ...
written 5.0 years ago by elvissober20 • updated 11 months ago by _r_am31k
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How to do BBmap batch processing correctly?
...   How to do BBmap batch processing correctly? Here is my bash code: cd /home/user/Documents/bbmap ./bbmap.sh ref=ref.fa # indexes fasta format file and sets reference filelist="fastaone.fasta, fastatwo.fasta, fastathree.fasta" for list in "$filelist" do ./bbmap.sh   May I also run it with in Py ...
software error wgs sequence sequencing pyth written 5.0 years ago by elvissober20

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