Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

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Comment: C: What is DeNovo Assembly?
... https://en.wikipedia.org/wiki/Sequence_assembly#De-novo_vs._mapping_assembly ...
written 1 day ago by Pierre Lindenbaum92k
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Answer: A: Eliminating calls for a particular chromosome, per sample, in a multisample VCF
... This kind of awk script will remove all the genotypes from your vcf for sample "S1" on any chromosome but the chromosome 2. Adjust it to your needs. Note that it doesn't change some values like "DP", .. in the INFO column. awk -F '\t' '/^#CHROM/ {split($0,header);} /^#/ {print;next;} /^2\t/ { ...
written 1 day ago by Pierre Lindenbaum92k • updated 1 day ago by WouterDeCoster16k
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Comment: C: Variant calling following multiple sequence alignment
... see: * https://github.com/sanger-pathogens/snp-sites * https://www.biostars.org/p/213586/ * https://www.biostars.org/p/49053/ * https://www.biostars.org/p/94573/ ...
written 2 days ago by Pierre Lindenbaum92k
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Answer: A: samtools updation in linux
... install from the sources: https://github.com/samtools/samtools/releases/tag/1.4 ...
written 2 days ago by Pierre Lindenbaum92k
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Answer: A: Print rows only if number matches
... The idea is to use awk insert a new normalized column for your two files: $ echo -e "a\tP415T\tb\na\tP415X\tb\na\tP415Y\tb" |\ awk -F '\t' '{key=$2; gsub(/[A-Z]$/,"",key); printf("%s\t%s\n",key,$0);}' |\ sort -t$'\t' -k1,1 P415 a P415T b P415 a P415X b P415 a P415Y b t ...
written 2 days ago by Pierre Lindenbaum92k
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Comment: C: Print rows only if number matches
... > . I want only those lines in which the number matches only with the next line not clear. ...
written 2 days ago by Pierre Lindenbaum92k
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Answer: A: extract DP of heterozygotes from vcf file
... Using bioalcidae: https://github.com/lindenb/jvarkit/wiki/BioAlcidae $ java -jar dist/bioalcidae.jar -e 'while(iter.hasNext()) { var vc=iter.next(),i=0;for(i=0;i< vc.getNSamples();++i) { var g=vc.getGenotype(i); if(!g.isHet()) continue; out.println(vc.getContig()+" "+vc.getStart()+" "+g.get ...
written 2 days ago by Pierre Lindenbaum92k
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Comment: C: Query related to GATK
... > Old PICARD 1.8.1 COMMAND: > > jar /home/yog/software/picard-1.8.1/src/main/java/picard/sam/CreateSequenceDictionary.java you're wrong. The old command was ``` java -jar /path/to/CreateSequenceDictionary.jar ## <- .jar NOT .java java is a compiled language ``` the new command is ...
written 2 days ago by Pierre Lindenbaum92k
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Answer: A: Mapping a chromosome position with Gene ID
... convert your files to BED format using **awk** and the use **bedtools intersect** to compute the intersection ...
written 3 days ago by Pierre Lindenbaum92k
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Answer: A: Generate bed file containing regions with no bigwig coverage
... > I would like to find regions in a bigwig file which do not have a score convert the wig to bedgraph : https://genome.ucsc.edu/goldenpath/help/bigWig.html use awk to filter out the region having a value lower than your treshold. also use 'bedtools complement' to find the regions not covered ...
written 3 days ago by Pierre Lindenbaum92k

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Popular Question 22 hours ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
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Scholar 3 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
Popular Question 3 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
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