Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

<prev • 8,617 results • page 3 of 862 • next >
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Answer: A: Genome and DNA - whats the correlation
... 1) we mean the whole genome, including the intergenic regions 2) No. what's a gene ? https://ghr.nlm.nih.gov/primer/basics/gene 3) https://ghr.nlm.nih.gov/primer/basics/gene; "What is a gene, post-ENCODE? History and updated definition." https://www.ncbi.nlm.nih.gov/pubmed/17567988 ; ...
written 19 days ago by Pierre Lindenbaum122k
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Comment: C: Any database of parasitic worm species?
... i think the identifiers come from several databases (? ) It could be in EOL (encyclopedia of life) while still being a worm... ...
written 19 days ago by Pierre Lindenbaum122k
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Answer: A: Any database of parasitic worm species?
... there is a **Species interaction datasets** database available for download at https://www.globalbioticinteractions.org/data.html $ wget -O - -q "https://depot.globalbioticinteractions.org/snapshot/target/data/tsv/interactions.tsv.gz" | gunzip -c | cut -f1,3,33,35,37 | grep -i parasite ...
written 19 days ago by Pierre Lindenbaum122k
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Comment: C: MergeSamFiles: Alignments added out of order in SAMFileWriterImpl.addAlignment f
... yeah, your sam are sorted... what would be the output of grep -w -F NbV1Ch01 *.sam | grep -w -E '(213308|213305)' ...
written 19 days ago by Pierre Lindenbaum122k
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Comment: C: How to convert a file to vcf format
... https://www.biostars.org/p/224702/ ...
written 19 days ago by Pierre Lindenbaum122k
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Comment: C: Move files that match the names on a list
... Hello genomes_and_MGEs! We believe that this post does not fit the main topic of this site. not related to bioinformatics. just a basic linux problem. https://stackoverflow.com/questions/41288970/ https://unix.stackexchange.com/questions/456444 For this reason we have closed your question. This ...
written 19 days ago by Pierre Lindenbaum122k
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Comment: C: Is it possible to output uncompressed FastQ files with bcl2fastq2 ?
... ok, I see. ...
written 19 days ago by Pierre Lindenbaum122k
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Comment: C: Is it possible to output uncompressed FastQ files with bcl2fastq2 ?
... > Imagine having 100 samples zipped, it would take like 4 days to unzip all of them. but you can do this in parallel. but most softwares like 'bwa' can read gzip files. ...
written 19 days ago by Pierre Lindenbaum122k
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Answer: A: How to convert a file to vcf format
... assuming the delimiter is a tab: run the following script for each file awk -f script .awk input.txt | bcftools view -O z -o out.vcf.gz with script.awk (add a '##contig' line for all your chromosomes) ``` BEGIN { FS="\t"; } /^CHROM/ { printf("##fileformat=VCFv4.2\n"); printf("##FORMAT= ...
written 19 days ago by Pierre Lindenbaum122k
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Comment: C: How to add rsIDs to VCF?
... > I've tried GATK VariantAnnotator and bcftools annotate as suggested by this post I found via Google, but I'm not having any luck. show us your command lines. ...
written 20 days ago by Pierre Lindenbaum122k

Latest awards to Pierre Lindenbaum

Popular Question 7 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Appreciated 7 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: Plotting Density Of Snps On Chromosomes
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Plotting Density Of Snps On Chromosomes
Scholar 10 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Scholar 11 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Appreciated 14 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 17 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
Scholar 17 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: Plotting Density Of Snps On Chromosomes
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
Good Answer 24 days ago, created an answer that was upvoted at least 5 times. For A: Plotting Density Of Snps On Chromosomes
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Appreciated 25 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Appreciated 25 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Good Answer 26 days ago, created an answer that was upvoted at least 5 times. For A: Plotting Density Of Snps On Chromosomes
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna
Scholar 29 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Plotting Density Of Snps On Chromosomes

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