Admin: Pierre Lindenbaum

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France/Nantes/Institut du Thorax - INSERM UMR1087
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http://plindenbaum.blo...
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Posts by Pierre Lindenbaum

<prev • 7,432 results • page 1 of 744 • next >
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Comment: C: Get variant position knowing the gene name, base change, and NM#
... see https://www.biostars.org/p/15992/ ; ...
written 12 hours ago by Pierre Lindenbaum108k
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Answer: A: Issue with Bcftools reheader
... the option -s of bcftools reheader is a **FILE** not a string. https://samtools.github.io/bcftools/bcftools.html -s, --samples FILE new sample names, one name per line, in the same order as they appear in the VCF file. Alternatively, only samples which need to be renamed can be listed ...
written 17 hours ago by Pierre Lindenbaum108k
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Comment: C: Software to calculate frequency of mutation by group
... If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. ![Upvote|Bookmark|Accept][1] [1]: http://i68.tinypic.com/2m2ykjr.png ...
written 19 hours ago by Pierre Lindenbaum108k
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Comment: C: GATK3 error message
... > your data is corrupted try to understand what I've done in my previous comment please https://www.biostars.org/p/321787/#321805 ...
written 21 hours ago by Pierre Lindenbaum108k
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Comment: C: GATK3 error message
... there is no problem with that resource. *your* data is corrupted. $ curl "ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta.gz" | gunzip -c | grep -v '^>' | tr -d '[ATGCNatgcn\n]' | grep -o '.' | sort | uniq -c 2 B 8 K ...
written 22 hours ago by Pierre Lindenbaum108k
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Comment: C: GATK3 error message
... what devon said: > your fasta file is likely corrupted, since it has a \ in it as a base. futhermore there is a 'O'. I also suggest you have a look at this fasta file: grep -n -A 5 -B 5 '/' ref.fasta ...
written 22 hours ago by Pierre Lindenbaum108k
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Answer: C: GATK3 error message
... what is the version of gatk ? what is the output of: grep -v '^>' /path/to/Homo_sapiens_assembly38.fasta | tr -d '[ATGCNatgcn\n]' | grep -o '.' | sort | uniq -c ...
written 23 hours ago by Pierre Lindenbaum108k
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Comment: C: Programming interview via Skype
... How to have technical and coding interviews over Skype https://blogs.skype.com/tips/2017/08/25/how-to-have-technical-and-coding-interviews-over-skype/?eu=true ...
written 1 day ago by Pierre Lindenbaum108k
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Comment: C: Downloading NCBI data with geographic location tag
... see https://www.biostars.org/p/221662/ ...
written 1 day ago by Pierre Lindenbaum108k
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Comment: C: Estimating cross contamination in a set of BAMS
... from twitter: https://twitter.com/m_foll/status/1009165148391661570 ...
written 1 day ago by Pierre Lindenbaum108k

Latest awards to Pierre Lindenbaum

Appreciated 17 hours ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 17 hours ago, created an answer with at least 3 up-votes. For A: Extracting List Of Genes Associated With A Pathway In Kegg
Scholar 17 hours ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Teacher 19 hours ago, created an answer with at least 3 up-votes. For A: Extracting List Of Genes Associated With A Pathway In Kegg
Scholar 19 hours ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Extracting List Of Genes Associated With A Pathway In Kegg
Scholar 2 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Appreciated 6 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 7 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Scholar 10 days ago, created an answer that has been accepted. For A: When Hard clipping is used instead of the Soft clipping ?
Scholar 10 days ago, created an answer that has been accepted. For A: Error in samtools view
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How To Extract Snps From A Desired List Of Gene Names
Scholar 11 days ago, created an answer that has been accepted. For A: Error in samtools view
Scholar 11 days ago, created an answer that has been accepted. For A: Error in samtools view
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: How To Extract Snps From A Desired List Of Gene Names
Scholar 12 days ago, created an answer that has been accepted. For A: Error in samtools view
Popular Question 13 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Scholar 13 days ago, created an answer that has been accepted. For A: Error in samtools view
Scholar 16 days ago, created an answer that has been accepted. For A: Error in samtools view
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: How To Extract Snps From A Desired List Of Gene Names
Scholar 21 days ago, created an answer that has been accepted. For A: Error in samtools view
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Ucsc Snp Genomic Positions (Duplicates And Wrong Positions)
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Ucsc Snp Genomic Positions (Duplicates And Wrong Positions)

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