Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

<prev • 7,274 results • page 1 of 728 • next >
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Comment: C: VCF file manipulation for extracting the required information
... **I'm sure this solution works** but, in the general case: allele = gt.split("/") doesn't work if the genotype is phased. int(data[1])+len(data[3])-2, doesn't work if there is a `INFO/END` if allele[0] == allele[1]: doesn't work if genotype is nocall `./.` or not diallelic ...
written 11 hours ago by Pierre Lindenbaum106k
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Comment: C: install of STAR
... Hello yueli7! We believe that this post does not fit the main topic of this site. just a PATH problem https://opensource.com/article/17/6/set-path-linux "Telling your Linux shell where to look for executable files is easy, and something everyone should be able to do." For this reason we have clo ...
written 12 hours ago by Pierre Lindenbaum106k
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Answer: A: VCF file manipulation for extracting the required information
... using bioalcidaejdk: http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html $ java -jar dist/bioalcidaejdk.jar -e 'stream().forEach(V->println(V.getContig()+" "+V.getStart()+" "+V.getEnd()+" "+V.getGenotype(0).getAlleles().stream().map(A->A.isCalled()?A.getDisplayString():".").collect(Collec ...
written 12 hours ago by Pierre Lindenbaum106k
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Comment: C: Merging two fastq.gz files
... not need to use `gzcat`, just use `cat` https://www.biostars.org/p/136025/ ...
written 14 hours ago by Pierre Lindenbaum106k
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Comment: C: Download multiple PDB from text file
... https://www.rcsb.org/pdb/static.do?p=download/web_download/download.jsp ?? ...
written 17 hours ago by Pierre Lindenbaum106k
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Comment: C: Reconstruct bed file out of columns
... what have you tried ? ...
written 18 hours ago by Pierre Lindenbaum106k
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Comment: C: How to call all the allele in samples
... how did you get call vcf from the bam ? bcftools ? gatk ? ...
written 21 hours ago by Pierre Lindenbaum106k
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Answer: A: How to check if BAM is indel-realigned?
... search a **program group** in the bam header for gatk IndelRealigner e.g:https://github.com/samtools/samtools/blob/9df632114a537f57928e4b2c17fbb1928679f877/test/dat/mpileup.1.sam @PG ID:bam_realignment_around_known_indels.1 PN:GenomeAnalysisTK PP:gatk_target_interval_creator.1 VN:1.2-29-g0acaf ...
written 1 day ago by Pierre Lindenbaum106k
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Comment: C: Create a library of fragments from restriction enzyme AAGCTT
... I don't know if it's going to work with javac 10, but try to add the source and target flags in https://github.com/lindenb/jvarkit/blob/master/Makefile#L885 ${JAVAC} -source 1.8 -target 1.8 -d ${tmp.dir} (....) and https://github.com/lindenb/jvarkit/blob/master/Makefile#L106 ${JAVAC} ...
written 1 day ago by Pierre Lindenbaum106k
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Comment: C: extract several fasta file with a list of ID (in order)
... this question has been asked a large number of times here. Please search for this question. Nevertheless, regarding your code, instead of doing your loop liste-nth times. How about scanning the fasta only one time and check if the current fasta name is in your `liste` ? ...
written 1 day ago by Pierre Lindenbaum106k

Latest awards to Pierre Lindenbaum

Scholar 1 day ago, created an answer that has been accepted. For A: Error in samtools view
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Search Motif In Raw Reads
Scholar 1 day ago, created an answer that has been accepted. For A: Error in samtools view
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Scholar 2 days ago, created an answer that has been accepted. For A: Error in samtools view
Popular Question 6 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Search Motif In Raw Reads
Scholar 8 days ago, created an answer that has been accepted. For A: Error in samtools view
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Scholar 13 days ago, created an answer that has been accepted. For A: Genomic Coverage - Samtool's undocumented "depth" verses the poorly documented p
Scholar 13 days ago, created an answer that has been accepted. For A: Error in samtools view
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Scholar 13 days ago, created an answer that has been accepted. For A: Error in samtools view
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Scholar 20 days ago, created an answer that has been accepted. For A: Error in samtools view
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