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Old 01-13-2011, 08:02 AM   #21
andrehorta
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Hi Laura!

Thank you very much with your attention! I need:

1) Download one genome from 1000 genomes project
2) I need use BRCA-DIAGNOSTIC or/and BOWTIE (i know how i use them, i follow the tutorial). I need to download other files to use BOWTIE?

Obs: I have linux, perl and other, the BOWTIE and BRCA-DIAGNOSTIC is run and ok in my computer.

Thank and sorry.
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Old 01-13-2011, 08:07 AM   #22
andrehorta
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Quote:
Originally Posted by laura View Post
The sequence_read dir contains the raw sequence reads that have been produced for a particular individual these are in fastq format.
The alignment dir contains alignment files in bam format which aligns the raw reads to a reference genome (in this case GRCh37).

There is more information about this data

http://www.1000genomes.org/data

thanks
How can i use this data with BOWTIE and BRCA-DIAGNOSTIC? What they will produce?
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Old 01-13-2011, 08:48 AM   #23
laura
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If you want to run alignments you need to download the data from the sequence read directory and align it to the genome.

I don't know how the program BRCA-Diagnotic works but it may be that you can just download the bam files from the alignment directory and work with those and then you don't need to run bowtie at all

I suspect you are likely to be more interested in the already discovered variants we released in November

ftp://ftp.1000genomes.ebi.ac.uk/vol1...lease/2010_11/
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Old 01-13-2011, 10:02 AM   #24
andrehorta
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Quote:
Originally Posted by laura View Post
If you want to run alignments you need to download the data from the sequence read directory and align it to the genome.

I don't know how the program BRCA-Diagnotic works but it may be that you can just download the bam files from the alignment directory and work with those and then you don't need to run bowtie at all

I suspect you are likely to be more interested in the already discovered variants we released in November

ftp://ftp.1000genomes.ebi.ac.uk/vol1...lease/2010_11/
OK, now i used SAMTOOLS to sort snp in HG00096.BAM and it's generated HG00096_snp.sorted.BAM. I need the HG000096.fna, e.g:

samtools pileup -cv -f genomes/NC_008253.fna ec_snp.sorted.bam
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Old 01-13-2011, 12:41 PM   #25
laura
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Okay I think this is the point it might be a good idea for you to explain what your ultimate aim as I imagine we will be able to give you more help that way

In answer to your particular question. These genomes are aligned to the reference genome GRCh37 and you can find the copy we used here ftp://ftp.1000genomes.ebi.ac.uk/vol1...cal/reference/
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Old 02-16-2011, 09:34 AM   #26
rstarke
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I'm having trouble finding information on how the high coverage exome data was generated for the 1K Genome main project. Not the targeted exon data that was part of the pilot phase, but the the full exome data that is partially available now. I want to be able to assess how good my alignments are, but need to know the exon capture method to find the intended target regions to do this. I could just use all RefSeq exons, or pick a specific exon capture kit's target list (like Nimblegen 2.1M), but it would be much better to have the real targets.
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Old 02-17-2011, 01:34 AM   #27
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The current target set for the 1000genomes exome sequencing can be found ftp://ftp.1000genomes.ebi.ac.uk/vol1...sus_exome_bed/
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Old 02-17-2011, 01:08 PM   #28
rstarke
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Thanks! This is just what i needed.
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