Admin: Pierre Lindenbaum
Pierre Lindenbaum ♦ 123k
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Posts by Pierre Lindenbaum
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... ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ ...
written 6 hours ago by
Pierre Lindenbaum ♦ 123k
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... I think OP only want the sequence from the BAM, not the REF. ...
written 9 hours ago by
Pierre Lindenbaum ♦ 123k
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... what kind of annotation ? don't you have a supervisor who can show you the way ? ...
written 9 hours ago by
Pierre Lindenbaum ♦ 123k
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... what is that code ? what is that language ? what are those files ? what is the context ? how is it related to bioinformatics ? https://www.biostars.org/p/357878/ ...
written 9 hours ago by
Pierre Lindenbaum ♦ 123k
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... cat samlist.txt | parallel --max-procs=5
parallel is cool but you'd better use a workflow manager (snakemake, nextflow, etc...) ...
written 1 day ago by
Pierre Lindenbaum ♦ 123k
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... yes there is a '@RG' but there is not sample (SM) associated to that RG. https://software.broadinstitute.org/gatk/documentation/article.php?id=6472
SM = Sample The name of the sample sequenced in this read group.
...
written 1 day ago by
Pierre Lindenbaum ♦ 123k
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... cat jeter.fa | paste - - | cut -f 1 | tr ";" "\n" | grep -F 'GeneID:' | cut -d ':' -f 2 | sort | uniq | while read G; do cat jeter.fa | paste - - | grep -F "GeneID:${G};" | tr "\t" "\n" | awk -v G=$G -F '[,;]' 'NR==1 {printf(">%s %s\n",G,$3);} (NR%2==0) {print}' ; done
>106680938 ...
written 1 day ago by
Pierre Lindenbaum ♦ 123k
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... root includes viruses. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi ...
written 1 day ago by
Pierre Lindenbaum ♦ 123k
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Answer:
A: Combine samples in bam/vcf
... a read group is set to a different sample name 'RG:SM' for each bam ( https://gatkforums.broadinstitute.org/gatk/discussion/6472/read-groups ) Use picard AddOrReplaceReadGroups http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups to change the read groups of your ...
written 1 day ago by
Pierre Lindenbaum ♦ 123k
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... Hello mathavanbioinfo!
We believe that this post does not fit the main topic of this site.
not related to bioinformatics. ask https://biology.stackexchange.com/ . Viruses use the host's translation machinery.
For this reason we have closed your question. This allows us to keep the site focused
o ...
written 2 days ago by
Pierre Lindenbaum ♦ 123k
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