Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

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Answer: A: Can someone provide me with vcf files with X and Y chromosomes? (Human)
... ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ ...
written 6 hours ago by Pierre Lindenbaum123k
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Comment: C: Reconstruct reference sequence from SAM file?
... I think OP only want the sequence from the BAM, not the REF. ...
written 9 hours ago by Pierre Lindenbaum123k
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Comment: C: help with exome analysis_only bam file
... what kind of annotation ? don't you have a supervisor who can show you the way ? ...
written 9 hours ago by Pierre Lindenbaum123k
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Comment: C: Increment numbers in a string for several iterations
... 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 Lindenbaum123k
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Comment: C: MarkDuplicates showing error, not recognising SM tag present in bam Header
... 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 Lindenbaum123k
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Answer: A: MarkDuplicates showing error, not recognising SM tag present in bam Header
... 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 Lindenbaum123k
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Answer: A: concat fasta sequences based on some common header string
... 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 Lindenbaum123k
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Answer: A: What is the difference between "root" and "cellular organisms" in NCBI taxonomy?
... root includes viruses. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi ...
written 1 day ago by Pierre Lindenbaum123k
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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 Lindenbaum123k
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Comment: C: Is there virus specific genetic code available?
... 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 Lindenbaum123k

Latest awards to Pierre Lindenbaum

Teacher 2 hours ago, created an answer with at least 3 up-votes. For A: Popular Sites For Asking Bioinformatics Questions?
Scholar 2 hours ago, created an answer that has been accepted. For A: Coverage Comparison Of Different Mappers
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Great Question 5 days ago, created a question with more than 5,000 views. For Mapping Snps To Pathways
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Popular Sites For Asking Bioinformatics Questions?
Scholar 9 days ago, created an answer that has been accepted. For C: BED file : error in naming chromosome's column
Scholar 9 days ago, created an answer that has been accepted. For A: how to edit a fasta file
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Scholar 9 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Appreciated 14 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
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Good Answer 16 days ago, created an answer that was upvoted at least 5 times. For A: Popular Sites For Asking Bioinformatics Questions?
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Scholar 22 days ago, created an answer that has been accepted. For A: Why do we need a .fai file and a .dict file of the reference during alignment an
Scholar 22 days ago, created an answer that has been accepted. For C: BED file : error in naming chromosome's column
Scholar 22 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Commentator 23 days ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
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Scholar 25 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Popular Sites For Asking Bioinformatics Questions?

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