This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Problem Using Tabix: Tabix Can'T Find The Directory Of The Example File

Hi everyone!

I am learning to use Tabix. I am interested in querying the structural genomic variations of 18 strains of mice stored on a Wellcome Trust Institute server ( ftp://ftp-mouse.sanger.ac.uk/REL-1302-SV/). The file has already been compressed using bgzip and indexed using tabix. The files are: 1) 18strains.REL-1302-SV.sdp.tab.gz 2) 18strains.REL-1302-SV.sdp.tab.gz.tbi (index)

According to the README file, I can simply type the following:

tabix  ftp://ftp-mouse.sanger.ac.uk/REL-110804-SV/18strains.REL-1302-SV.sdp.tab.gz  2:3000000-4000000

However, when I do so, I get the following error on my terminal:

trains.REL-1302-SV-GRCm38.sdp.tab.gz  2:3000000-4000000
[kftp_connect_file] 550 /REL-1302-SV/18strains.REL-1302-SV-GRCm38.sdp.tab.gz: No such file or directory
[main] fail to open the data file.

Does anyone else have similar issues?

Thank you!

tabix
• 3,187 views • link
updated by Neilfws Neilfws • written by Johnathan • Johnathan

1 answer

just look at ftp://ftp-mouse.sanger.ac.uk/REL-110804-SV: the file has been deleted.

try to play with the files under ftp://ftp-mouse.sanger.ac.uk/REL-110804-SV/all/

• 36 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Thank you for your input. Yes, you are right. I didn't verify this at first because I was following the HELPME file. However, I simply downloaded the file from another path onto my computer and tabix works great now.

• 0 views • link
written by Johnathan • Johnathan

Log in to answer this question.

More posts like this
  • Known-variant and AF-only files of GATK Mutect2 on Mouse DNA sequencing data
    written by whb • whb
    I have some mouse C57 targeted panel sequencing data. I want to call somatic variants using GATK. Because of the cost, there are only 4 …
  • 1000G Query / Using Tabix With A Proxy
    written by secretjess secretjess
    <p>When I run the following command the connection times out:</p> <pre><code>./tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 1:57000000-57001000 &gt; test.vcf connect: Connection timed out [main] fail to open the …
  • Variant Effect And The Impact Of Samples
    written by User 1933 • User 1933
    <p>I have extracted a region from 1KG webserver like </p> <pre><code>mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -N -e 'select concat("ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/ALL.",K.chrom,".phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz"),concat(RIGHT(K.chrom,LENGTH(chrom)-3),":",MIN(K.txStart)+1,"-",MAX(K.txEnd)) from knownGene as K,kgXref as …
  • Sra-Pileup Question
    written by Sergei Lebedev • Sergei Lebedev
    <p>I'm having trouble extracting a <a href='http://samtools.sourceforge.net/pileup.shtml'>pileup</a> file from an <a href='ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX101/SRX101206/SRR364089/SRR364089.sra'>SRA</a> using <code>sra-pileup</code> command. NCBI <a href='http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&amp;f=sra-pileup'>documentation</a> only covers command line arguments for the …
  • How To Run Tabix Locally
    written by Peixe Peixe
    <p>I have a local <code>vcf</code> file on my computer (<em>it is actually the full chromosome 22</em>). I would like to subset it in regions. I …
  • Reindex A Vcf File / How To Handle Cosmic Vcf Files
    written by secretjess secretjess
    <p>So I have managed to successfully query 1000 Genome VCF files before by following tutorials, I thought I could apply this to the COSMIC database. …
  • Parsing A Vcf File On An Ftp Server Using Single-Line Perl
    written by soosus • soosus
    <p>Sanger recently released mouse SNPs (in VCF format) from next-generation sequencing for 18 strains. I need to get and parse (without downloading the huge file) …
  • How To Interpret Ciend And Cipos Fields In Vcf Files From 1000 Genomes?
    written by agnieszka • agnieszka
    <p>Here is an example variant for genome NA20317. It comes from 1000 genomes data (file: <a href='ftp://ftp.ncbi.nih.gov///1000genomes/ftp/release/20110521/ALL.chr8.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz'>ftp://ftp.ncbi.nih.gov///1000genomes/ftp/release/20110521/ALL.chr8.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz</a>) and was obtained with tabix and vcf-subset script:</p> …
  • Problems Accessing 1000G Data
    written by Ahdf-Lell-Kocks • Ahdf-Lell-Kocks
    <p>I am just copy+pasting from the 1000g instructions here: <br/> <a href="http://www.1000genomes.org/faq/how-do-i-get-sub-section-bam-file">http://www.1000genomes.org/faq/how-do-i-get-sub-section-bam-file</a></p> <pre><code>samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 17:7512445-7513455 </code></pre> <p>But I can't get it to work:</p> …
  • Using Tabix And Vcf Tools To Get Cnv / Sv Frequencies From 1000 Genomes Data
    written by Ryan D Ryan D
    <p>I read this <a href='http://biostar.stackexchange.com/questions/6920/getting-allele-frequencies-from-1000-genomes'>excellent post</a> by Stephen on getting data from 1000 genomes with tabix, but it seems to not be working for me. …