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  • simthecao2021
    replied
    the topic very good. Thanks bro

    Leave a comment:


  • corintio45
    replied
    A relatively complete set of variant and other files associated.

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  • lucasrocha
    replied
    A Fast Algorithm for th inexact Characteristic String Problem - Doubt

    Hi Guys,

    Fine?

    Has anyone read this article?
    Https://mediatum.ub.tum.de/doc/1094391/1094391.pdf

    I have question about ring buffer of this article...

    The page 11/12 the article explains for us that algorithm acess lines 14 and 15 of algorithm and posErr is with value k+1, but I was testing and the value is k and the algoritm Assumes negative values ​​for the ring buffer posErr....

    Can someone who knows this problem help me understand how to work with this ring buffer, or am I analyzing it wrong?

    Thanks

    Leave a comment:


  • laura
    replied
    Start a new thread, this is not the right place for this question

    Leave a comment:


  • Mokhtar
    replied
    Please is there any one can help me how can I BLAST one FASTE file with more than 3000 DNA sequences generated from fungus community.

    Leave a comment:


  • laura
    replied
    Mokhtar you would be better creating a new thread for your question, this isnt really related to the 1000 genomes project

    If you let people know what your sequences (dna, cdna, protein?) are and what species you are working in they will probably be able to offer better advice

    Leave a comment:


  • Mokhtar
    replied
    Please is there any one can help me how can I BLAST one FASTE file with more than 3000 sequences

    Leave a comment:


  • jgibbons1
    replied
    @papori I had the same issue. You can download the "sequence.index" file from the ftp site (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/). In Excel, I ended up making a new column where I divided BASE_COUNT by READ_COUNT. You can then filter the read length you are looking for.

    Leave a comment:


  • laura
    replied
    These two data sets represent our most recent set of alignments and the frozen alignments used for the phase1 analysis effort

    There will be overlapping individuals between the two sets but no bam files should be the same as an extended version of GRCh37 is being used for the post phase1 mapping

    see http://www.1000genomes.org/faq/which...bly-do-you-use

    You should be able to tell the difference between these files by the YYYYMMDD in their name as this points to the sequence index they were based on

    Leave a comment:


  • southan
    replied
    I'm going to download Bam files from the Project.
    I see two links:
    ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/
    and
    ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/

    There are some overlapping files between the two links.

    I would like to know which one I should use?

    Thanks,

    Leave a comment:


  • papori
    replied
    Hi,
    Sorry if this is already been asked, I didn't find it..

    I try to figure out if I can do a search by read length.
    I am looking for reads length 101.
    Is there a way to know this information before downloading?
    I looked in the sequence.index but I didn't find this.

    Thanks in advance,
    Pap

    Thanks,

    Leave a comment:


  • rama
    replied
    Thanks Laura, for trying it out.

    Leave a comment:


  • laura
    replied
    Hello Rama

    Unfortunately I can not recreate your issue

    Using your command I get a vcf file which just contains genotypes for NA10851

    Leave a comment:


  • rama
    replied
    Hi Laura,

    I am still having trouble with extracting the variant calls of a specific sample.

    As you pointed out earlier that I have downloaded sites file with no genotype column, so now I got this version ALL.2of4intersection.20100804.genotypes.vcf.gz vcf and tbi file from ftp site (release/20100804).

    and I used the following command to subset the vcf file

    tabix -fh /Volumes/Macintosh_HD_3/1000Genome/ALL.2of4intersection.20100804.genotypes.vcf.gz 1 | perl ~/othertools/vcftools_0.1.10/perl/vcf-subset -c NA10851 > NA10851/NA10851_chr1

    but strangely the out-put file has all genotype columns. I have been following the directions given on the 1000 genome except the I don't give the range for chromosome as I want to get all variants. So I tried with giving the coordinates (see below) and result file has just the header only.

    here is the command i used,
    tabix -fh /Volumes/Macintosh_HD_3/1000Genome/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:1-243199373 | perl ~/othertools/vcftools_0.1.10/perl/vcf-subset -c NA10851 > NA10851/NA10851_chr2

    so now I really don't know what I am doing wrong in trying to subset the vcf file. I really appreciate for your kind help so far and would be very grateful if you could help me how to solve this.

    thank you so much.
    Rama

    Leave a comment:


  • laura
    replied
    You need to give tabix some sort of chromosome name otherwise it doesn't know what to fetch

    If you just want to filter the whole file you will need to use zcat

    That being said you downloaded the sites file which contains no genotype info and no columns with individual genotypes to filter

    Leave a comment:

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