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Admin: Pierre Lindenbaum

gravatar for Pierre Lindenbaum
Reputation:
129,240
Status:
Trusted
Location:
France/Nantes/Institut du Thorax - INSERM UMR1087
Website:
http://plindenbaum.blo...
Twitter:
yokofakun
Scholar ID:
Google Scholar Page
Last seen:
57 minutes ago
Joined:
10 years, 5 months ago
Email:
p**********@yahoo.fr

Bioinformatics , Genetics

http://twitter.com/yokofakun

http://plindenbaum.blogspot.com

https://github.com/lindenb/jvarkit

 

 

Posts by Pierre Lindenbaum

<prev • 9,374 results • page 1 of 938 • next >
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Comment: C: Replace matching sections of two fastas
... join -t $'\t' -v 1 -1 1 -2 1 file1.tsv file2.tsv > only_in_1.tsv ...
written 9 hours ago by Pierre Lindenbaum ♦ 129k
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Comment: C: Paired-End Reads and Variant Calling
... By the way, it's always a bad idea to align the read on only one chromosome rather than on the whole reference. ...
written 1 day ago by Pierre Lindenbaum ♦ 129k
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Comment: C: Paired-End Reads and Variant Calling
... This is a problem with the way your reads are ordered in the two fastq. Both files should have the read same names and in the very same order. ...
written 1 day ago by Pierre Lindenbaum ♦ 129k
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Comment: C: Paired-End Reads and Variant Calling
... what are the error/messages displayed ? ...
written 1 day ago by Pierre Lindenbaum ♦ 129k
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Comment: C: grep -v command
... @genomax opps, updated. ![https://xkcd.com/745/][1] [1]: https://imgs.xkcd.com/comics/dyslexics.png ...
written 1 day ago by Pierre Lindenbaum ♦ 129k
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Answer: A: grep -v command
... > Hi, I have a BED file having entries from all chromosome and would like to remove chr1 while retaining all other entires which start with chr11 chr19 and so on using grep is not a good choice. Because the word 'chr1' could be present in another column. using awk: awk '$1!="chr1"' input. ...
written 1 day ago by Pierre Lindenbaum ♦ 129k
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Answer: A: filtered tab delimited file with awk
... awk -F '[ "\t]+' '{for(i=9;i+1<=NF;i++) if($i=="FPKM" && $(i+1)>=0.5) {print;break;}}' yourfile ...
written 2 days ago by Pierre Lindenbaum ♦ 129k
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Answer: A: Replace matching sections of two fastas
... - [linerize both fasta files][1] - remove the '/rc' suffix with `sed` - use `sort` to sort both linearized files on the sequence name. - use `join` to select the sequences present in linearized1 but not in linerarized2 - use `join` to select the sequences in linearized1 and in linerariz ...
written 2 days ago by Pierre Lindenbaum ♦ 129k
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Comment: C: Finding unique variants in a vcf
... see GATK [selectvariants][1] with a [JEXL expression][2]. e.g: !vc.getGenotype("sample1").isHomRef() && (vc.getGenotype("sample2").isHomRef() && vc.getGenotype("sample3").isHomRef()) [1]: https://gatk.broadinstitute.org/hc/en-us/articles/360037055952-SelectVariants [2]: h ...
written 2 days ago by Pierre Lindenbaum ♦ 129k
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Comment: C: A:orthomcl with local mysql server on linux server, complete install
... This post was cited in: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008104 > Regional sequence expansion or collapse in heterozygous genome assemblies ...
written 3 days ago by Pierre Lindenbaum ♦ 129k

Latest awards to Pierre Lindenbaum

Appreciated 1 day ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Great Question 14 days ago, created a question with more than 5,000 views. For Exome Aggregation Consortium (ExAC) database ?
Appreciated 14 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 28 days ago, created an answer that has been accepted. For A: bcftools view VCF parse error
Appreciated 28 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Scholar 4 weeks ago, created an answer that has been accepted. For A: bcftools view VCF parse error
Scholar 4 weeks ago, created an answer that has been accepted. For A: bcftools view VCF parse error
Appreciated 4 weeks ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 5 weeks ago, created an answer that has been accepted. For A: bcftools view VCF parse error
Scholar 5 weeks ago, created an answer that has been accepted. For A: quality check of bam files
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Scholar 6 weeks ago, created an answer that has been accepted. For A: quality check of bam files
Appreciated 6 weeks ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Ngs And Recalibration
Scholar 7 weeks ago, created an answer that has been accepted. For A: quality check of bam files
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Appreciated 8 weeks ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 8 weeks ago, created an answer that has been accepted. For A: quality check of bam files
Scholar 8 weeks ago, created an answer that has been accepted. For A: quality check of bam files
Scholar 8 weeks ago, created an answer that has been accepted. For A: quality check of bam files
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Choosing Random Set Of Seqs From Larger Set
Great Question 8 weeks ago, created a question with more than 5,000 views. For Exome Aggregation Consortium (ExAC) database ?
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