Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

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Comment: C: GATK SPlitNCigarReads memory issue
... Posted on GATK forum: http://gatkforums.broadinstitute.org/gatk/discussion/8848/ ...
written 2 hours ago by Pierre Lindenbaum88k
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Comment: C: Extract amino acid sequence (with fasta header) from FGENESH tool : Python
... please flag this as answered (green flag on the left) ...
written 2 hours ago by Pierre Lindenbaum88k
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Comment: C: How to delete two populations pseudo snps from a mutiple populations vcf file?
... > the original vcf file was divided into 3 sub-vcf files why ? asking because all the information is already here. Why do you need to remove some samples ? ...
written 2 hours ago by Pierre Lindenbaum88k
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Comment: C: file format for joimap
... what is joinmap format ? ...
written 3 hours ago by Pierre Lindenbaum88k
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Answer: A: Extract amino acid sequence (with fasta header) from FGENESH tool : Python
... grep line starting with '>' and print one line After the match grep '^>' -A 1--no-group-separator input.txt ...
written 4 hours ago by Pierre Lindenbaum88k
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Answer: A: Searching nucleotide databases for term with special character
... >searching for a term to be included in the organism name. It has the format [PREFIX]:[number] wget -O taxdmp.zip ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip unzip taxdmp.zip names.dmp $ grep -E '\:[0-9]+' names.dmp | grep "scientific name" | tail 1897030 | Firmicute ...
written 5 hours ago by Pierre Lindenbaum88k
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Comment: C: Searching nucleotide databases for term with special character
... which database/field are you searching ? If it's a DNA sequence, it would be easier to scan the files from a FTP server... ...
written 6 hours ago by Pierre Lindenbaum88k
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Answer: A: kaas standalone installation
... ftp://ftp.kuicr.kyoto-u.ac.jp/moriya/kaas_sa/index.html # system require ==================== perl 5.8 or later (threads Symbol) ruby 1.8 or later NCBI BLAST (legacy_blast or blast+) HMMER 3 (linux commands; wget, wc, rm, etc.) # setup =============== ...
written 8 hours ago by Pierre Lindenbaum88k
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Answer: A: Split VCF file
... RandomlySplitVariants https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_RandomlySplitVariants.php ...
written 23 hours ago by Pierre Lindenbaum88k
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Comment: C: Retrieving species information from ensembl bacteria in JSON doesn't work
... JSON works for me: ``` $ wget -O - "http://rest.ensemblgenomes.org/info/species?content-type=application/json;compara=bacteria" | wc -c --2017-01-17 19:10:10-- http://rest.ensemblgenomes.org/info/species?content-type=application/json;compara=bacteria Resolving rest.ensemblgenomes.org (rest.ensembl ...
written 23 hours ago by Pierre Lindenbaum88k

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Scholar 5 hours ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
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Popular Question 4 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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Scholar 22 days ago, created an answer that has been accepted. For A: Finding Variants in BAM file reads with mpileup
Scholar 22 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
Popular Question 22 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 28 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
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Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream

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