Admin: Pierre Lindenbaum

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

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Answer: A: Meaning of "EX_TARGET" in VCF files 1000 genomes
... curl -s "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" | gunzip -c | grep "EX_TARGET" -m1 ##INFO= > indicates whether a variant is within the exon pull down target boundaries ...
written 1 day ago by Pierre Lindenbaum94k
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Comment: C: Is there any risk of having my research scooped after posting my manuscript onto
... Hello zengxi.hada! We believe that this post does not fit the main topic of this site. not related to bioinformatics. ask https://academia.stackexchange.com/ For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. ...
written 3 days ago by Pierre Lindenbaum94k
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Comment: C: How to plot SNPs along a chromosome?
... > Given the positions of the SNPs in the contigs of the alignment, what is this file ? does it contains CHROM and POS ? > I'm now trying to plot the distribution of found variants along each chromosome. if so, why do you need the other steps ? Mummer3 etc... ? ...
written 3 days ago by Pierre Lindenbaum94k
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Answer: A: Circos histogram from SNP.VCf file
... * using **awk** get the chrom/start of the VCF, group the pos by windows of 10000 * **sort** / **uniq** to get the count of variants in each window of 10000 bp * use awk to create chrom/start/end/count . The chrom must be the same than in the circos karyotype/config, that's with I why I've added a ' ...
written 3 days ago by Pierre Lindenbaum94k
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Comment: C: Circos histogram from SNP.VCf file
... histogram of what ? variant per Mb ? per sample/genotypes Mb ? ...
written 4 days ago by Pierre Lindenbaum94k
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Comment: C: Annotation table of enzymes (IntEnz, ..)
... and what is this ENGXXXXX1 ? I cannot see this in your URL ...
written 4 days ago by Pierre Lindenbaum94k
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Answer: A: where is latest omim.txt.Z?
... OMIM is no longer part of the NCBI. see https://www.omim.org/ I'm not even sure, this file omim.txt.Z is still generated: https://omim.org/downloads/ ...
written 5 days ago by Pierre Lindenbaum94k
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Comment: C: Annotation table of enzymes (IntEnz, ..)
... > the BioPAX format is not quite straight forward to process. where is this file please ? ...
written 5 days ago by Pierre Lindenbaum94k
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Comment: C: How to extract reads with no INDEL?
... please check the green marks on the left to validate+close the question ...
written 6 days ago by Pierre Lindenbaum94k
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Answer: A: How can I extract base on specific loci from all reads overlapping that?
... using sam2tsv : http://lindenb.github.io/jvarkit/Sam2Tsv.html $ java -jar dist/sam2tsv.jar ~/scf7180000354095.bam -R ~/scf_7180000354095.fasta #READ_NAME FLAG CHROM READ_POS BASE QUAL REF_POS REF OP HISEQ:348:H2YWCBCXX:1:1115:19355:8 ...
written 6 days ago by Pierre Lindenbaum94k

Latest awards to Pierre Lindenbaum

Scholar 1 day ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 1 day ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 8 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 10 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 11 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Popular Question 11 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Scholar 12 days ago, created an answer that has been accepted. For A: Calculating Coverage Using CIGAR String
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Scholar 19 days ago, created an answer that has been accepted. For A: Calculating Coverage Using CIGAR String
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Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: How To Get Gene Regions +3Kb Upstream

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