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 • 9,322 results • page 3 of 933 • next >
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Comment: C: Reverse Complement of each coding regions
... > Complement but here I need to find for each CDS I understand the question as :" I want to find all the ORFs in the reverse complement." ...
written 11 days ago by Pierre Lindenbaum129k
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Comment: C: Reverse Complement of each coding regions
... http://emboss.sourceforge.net/apps/cvs/emboss/apps/transeq.html > transeq reads one or more nucleotide sequences and writes the corresponding protein sequence translations to file. It can translate in any of the 3 forward or three reverse sense frames, or in all three forward or reverse frames, ...
written 12 days ago by Pierre Lindenbaum129k
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Answer: A: Detection nucleotide changes in VCF file
... bcftools view --no-header -i 'REF=="A" && ALT=="T" ' input.vcf | wc -l or using awk awk -F '\t' '($4=="A" && $5=="T" && !($0 ~ /^#/))' input.vcf | wc -l ...
written 12 days ago by Pierre Lindenbaum129k
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Comment: C: Intersect exome region from whole genome gvcf
... yes and yes ...
written 13 days ago by Pierre Lindenbaum129k
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Comment: C: Convert .sam to .bam without producing writing .sam file to storage space
... > without producing writing .sam file to storage space? what does that mean ? ...
written 14 days ago by Pierre Lindenbaum129k
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Answer: A: Is there a tool to find the correct percentage of duplication levels in FastQ ?
... brute force method (word-size=8). Good luck with that if your fastq is big. gunzip -c input.fq.gz | \ awk '(NR%4==2) {L=length($0);W=8;for(i=1;i+W<=L;i++) {print substr($0,i,W);}}' |\ LC_ALL=C sort -T . | uniq -c |\ sort -nr |\ head ...
written 14 days ago by Pierre Lindenbaum129k
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Comment: C: Intersect exome region from whole genome gvcf
... I got the same problem, at the end I moved back to gatk/CombineGVCF ... ...
written 14 days ago by Pierre Lindenbaum129k
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Answer: A: change the field separator in R or awk
... depends of the context : use awk+gsub https://www.gnu.org/software/gawk/manual/html_node/String-Functions.html if it's a token among multiple columns. just use ` tr` if it's the whole line. ...
written 14 days ago by Pierre Lindenbaum129k
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Comment: C: BED coordinates for short DNA sequences (gRNA)
... > I have >700 gRNAs and don't really want to run BLAT 28 times run the standalone version of blat.... ...
written 15 days ago by Pierre Lindenbaum129k
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Comment: C: codon changes finding in gene
... you **just** have to reformat your input. Molecular biology is 90% moving small liquids from one tube to another. Computational biology is 90% file manipulation.— Stephen Williams (@SvenAT) August 2, 2016 ...
written 18 days ago by Pierre Lindenbaum129k

Latest awards to Pierre Lindenbaum

Teacher 4 days 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 days ago, created an answer that has been accepted. For A: bcftools view VCF parse error
Scholar 4 days ago, created an answer that has been accepted. For A: bcftools view VCF parse error
Appreciated 4 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: bcftools view VCF parse error
Scholar 9 days ago, created an answer that has been accepted. For A: quality check of bam files
Teacher 12 days 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 16 days ago, created an answer that has been accepted. For A: quality check of bam files
Appreciated 17 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Popular Question 19 days ago, created a question with more than 1,000 views. For Ngs And Recalibration
Scholar 20 days ago, created an answer that has been accepted. For A: quality check of bam files
Teacher 21 days 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 23 days 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 26 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 26 days ago, created an answer that has been accepted. For A: quality check of bam files
Scholar 26 days ago, created an answer that has been accepted. For A: quality check of bam files
Scholar 29 days ago, created an answer that has been accepted. For A: quality check of bam files
Good Answer 29 days ago, created an answer that was upvoted at least 5 times. For A: Choosing Random Set Of Seqs From Larger Set
Great Question 4 weeks ago, created a question with more than 5,000 views. For Exome Aggregation Consortium (ExAC) database ?
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
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Choosing Random Set Of Seqs From Larger Set
Appreciated 4 weeks ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Choosing Random Set Of Seqs From Larger Set
Teacher 5 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 5 weeks ago, created an answer that has been accepted. For A: Parsing a portion of a fasta file header

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