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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yokofakun
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9 years, 10 months ago
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Posts by Pierre Lindenbaum

<prev • 8,901 results • page 1 of 891 • next >
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Answer: A: Is it possible to remove reads from BAM which match the reference at a position
... Using samjdk: http://lindenb.github.io/jvarkit/SamJdk.html and the following snippet. final boolean accept=true; final String contig="RF02"; final byte base='A'; final int position=877; if(record.getReadUnmappedFlag()) return accept; if(!record.getContig().equals( ...
written 1 hour ago by Pierre Lindenbaum125k
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Comment: C: Modifying fastq base at specific reference location on different length reads
... please flag the question as answered if it fulfills your needs (green tick on the left) ...
written 1 hour ago by Pierre Lindenbaum125k
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Comment: C: experimentally validated protein protein interactions
... see https://string-db.org/cgi/download.pl in the **SQL** dump evidence_schema.v11.0.sql.gz (13.2 Gb) ...
written 4 hours ago by Pierre Lindenbaum125k
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Comment: C: IGV viewer could not display genome sequences correctly
... how was formatted you fasta sequence can you verifiy that the chromosome is present in the *.fasta , *.fai and the *.dict files. ...
written 21 hours ago by Pierre Lindenbaum125k
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Answer: A: Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vc
... using vcffilterjdk: http://lindenb.github.io/jvarkit/VcfFilterJdk.html java -jar dist/vcffilterjdk.jar -rc -e 'return new VariantContextBuilder(variant).genotypes( variant.getGenotypes().stream().map(G->{ if(!G.hasAD() || !G.isHet()) return G; final int ad[]=G.getAD(); if(ad.length!=2) ret ...
written 22 hours ago by Pierre Lindenbaum125k
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Answer: A: Literature text exploration to display statistics in Pubmed
... using eutils $ seq 2000 2020 | while read Y ; do wget -q -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer[TIAD]+${Y}[PDAT]&rettype=count" | xmllint --xpath '/eSearchResult/Count/text()' - && echo " $Y"; done 70841 2000 73077 2001 ...
written 1 day ago by Pierre Lindenbaum125k
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Comment: C: Phobius plot - unrecognized terminal option
... please mark the question as answered, (green mark on the left) ...
written 1 day ago by Pierre Lindenbaum125k
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Comment: C: Phobius plot - unrecognized terminal option
... try to change this line: https://github.com/JamesABaker/complexity_in_pymol/blob/46b044d13b7930455878aab42e1fbdfd3f05eea4/pymol/phobius.pl#L32 ...
written 1 day ago by Pierre Lindenbaum125k
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Answer: A: Phobius plot - unrecognized terminal option
... As far as I can see there is not such option "**color**" in gnuplot: http://gnuplot.sourceforge.net/docs_4.2/node409.html set terminal png {{no}transparent} {{no}interlace} {{no}truecolor} {rounded|butt} {tiny | small | medium | large | giant} { ...
written 1 day ago by Pierre Lindenbaum125k
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Answer: C: Modifying fastq base at specific reference location on different length reads
... > or script that can use a sam file aligned to a consensus where I can modify the base at a specific location see https://www.biostars.org/p/404363 ...
written 1 day ago by Pierre Lindenbaum125k

Latest awards to Pierre Lindenbaum

Scholar 1 day ago, created an answer that has been accepted. For A: Extract coverage information from IGV
Scholar 2 days ago, created an answer that has been accepted. For A: Extract coverage information from IGV
Scholar 3 days ago, created an answer that has been accepted. For A: Extract coverage information from IGV
Appreciated 3 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Gene Ontology - Go Id To Terms, Term Definitions, Name, Etc
Scholar 3 days ago, created an answer that has been accepted. For A: Extract coverage information from IGV
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Gene Ontology - Go Id To Terms, Term Definitions, Name, Etc
Scholar 4 days ago, created an answer that has been accepted. For A: Extract coverage information from IGV
Scholar 7 days ago, created an answer that has been accepted. For A: Extract coverage information from IGV
Scholar 7 days ago, created an answer that has been accepted. For A: Extract coverage information from IGV
Scholar 7 days ago, created an answer that has been accepted. For A: Extract coverage information from IGV
Good Answer 7 days ago, created an answer that was upvoted at least 5 times. For A: Bioinformatic Cartoon
Appreciated 7 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: Extract coverage information from IGV
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Gene Ontology - Go Id To Terms, Term Definitions, Name, Etc
Scholar 10 days ago, created an answer that has been accepted. For A: Coverage Comparison Of Different Mappers
Scholar 21 days ago, created an answer that has been accepted. For A: Coverage Comparison Of Different Mappers
Appreciated 23 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Great Question 28 days ago, created a question with more than 5,000 views. For Exome Aggregation Consortium (ExAC) database ?
Appreciated 4 weeks 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: Gene Ontology - Go Id To Terms, Term Definitions, Name, Etc
Scholar 5 weeks ago, created an answer that has been accepted. For A: Coverage Comparison Of Different Mappers
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Gene Ontology - Go Id To Terms, Term Definitions, Name, Etc
Scholar 5 weeks ago, created an answer that has been accepted. For A: Coverage Comparison Of Different Mappers
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Bioinformatic Cartoon

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