Admin: Pierre Lindenbaum

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France/Nantes/Institut du Thorax - INSERM UMR1087
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Posts by Pierre Lindenbaum

<prev • 8,616 results • page 1 of 862 • next >
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Comment: C: Delete character from sequence id
... just cut: cut -d '_' -f 1,2 in.fasta ...
written 5 days ago by Pierre Lindenbaum122k
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Comment: C: Extracting sequence less than N length from FASTA file
... Hello atitparajuli2018! Questions similar to yours can already be found at: How To Filter Multi Fasta By Length?? Perl How To Isolate Fasta Sequences With A Range Of Values Filter DNA sequence in FASTA file by minimum length and redirect sequences that don't meet condition to new file u ...
written 6 days ago by Pierre Lindenbaum122k
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Comment: C: How I update makeblastdb
... did you set the PATH ? https://www.cyberciti.biz/faq/unix-linux-adding-path/ ...
written 6 days ago by Pierre Lindenbaum122k
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Answer: A: Analyzing VCF file
... you could use https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php with `-an DP` but it is a bad idea for exomes : https://software.broadinstitute.org/gatk/documentation/article?id=11084 > Depth ...
written 6 days ago by Pierre Lindenbaum122k
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Answer: A: understanding the data from the ucsc table browser of hg19, including gene distr
... > I need to find the intron length from this data. length of ith intron: intronLength += $exonStarts[ith+1] - $exonEnds[ith] ) ...
written 7 days ago by Pierre Lindenbaum122k
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Answer: A: Paired-end reads that span a position in an assembly
... using samjdk. http://lindenb.github.io/jvarkit/SamJdk.html Say you want spanning RF01:1000-2000. samtools view -u S1.bam RF01 | java -jar dist/samjdk.jar -e 'if(record.getReadUnmappedFlag() || !record.getReadPairedFlag() || record.getMateUnmappedFlag() || !record.getContig().equals(record.getM ...
written 7 days ago by Pierre Lindenbaum122k
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Comment: C: Extracting reads mapping to CDS regions but not the first 45bp after ATG
... > also remove the last 5 codons should be something like positions.subList(45,positions.size()-15); for + strand. The function sublist is https://docs.oracle.com/javase/8/docs/api/java/util/List.html#subList-int-int- ...
written 8 days ago by Pierre Lindenbaum122k
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Comment: C: Extracting reads mapping to CDS regions but not the first 45bp after ATG
... ENST00000442639 is discarded because there is no stop codon (Incomplete CDS) http://www.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000134321;r=2:6865828-6887053;t=ENST00000442639 ...
written 8 days ago by Pierre Lindenbaum122k
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Answer: A: Extracting reads mapping to CDS regions but not the first 45bp after ATG
... using BioAlcidaeJdk http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html https://gist.github.com/lindenb/372571a0952e9ad19b07ce499c46fab1 (not checked) $ java -jar dist/bioalcidaejdk.jar -F GTF -f bioalcidae.code Homo_sapiens.GRCh37.87.gtf.gz 3 57557938 57558025 ENST00000303436 ...
written 8 days ago by Pierre Lindenbaum122k

Latest awards to Pierre Lindenbaum

Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: Plotting Density Of Snps On Chromosomes
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Plotting Density Of Snps On Chromosomes
Scholar 6 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Scholar 8 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Appreciated 11 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Scholar 14 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: Plotting Density Of Snps On Chromosomes
Commentator 20 days ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
Good Answer 21 days ago, created an answer that was upvoted at least 5 times. For A: Plotting Density Of Snps On Chromosomes
Commentator 21 days ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Appreciated 22 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Appreciated 22 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: Plotting Density Of Snps On Chromosomes
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Scholar 26 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Commentator 28 days ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
Commentator 29 days ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Plotting Density Of Snps On Chromosomes
Scholar 29 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Scholar 4 weeks ago, created an answer that has been accepted. For A: how to edit a fasta file

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