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Old 10-09-2011, 10:59 AM   #1
efoss
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Location: Seattle

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Default confused by all the 1000 Genomes fastq files

I would like to get data from the main 1000 Genomes project (not just the pilot project). I would like to get exome fastq files. I go to their ftp site here (in this case to get data for NA11843):

ftp://ftp-trace.ncbi.nih.gov/1000gen...sequence_read/

I see a ton of fastq files in here and I'm having trouble figuring out what is what. Are any of these exome capture data, and if so, which ones? I've dug around a lot trying to find this information, but somehow I just can't find it. I assume that there must be exome data in here, in part because this same person has alignment files in this path:

ftp://ftp-trace.ncbi.nih.gov/1000gen...ome_alignment/


Thank you.

Eric
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Old 10-10-2011, 03:42 AM   #2
sfck8686
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Smile exome alignment

Hi
In my opinion, maybe you can find the data on the site:
ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA*****/exome alignment.

Hope to be helpful for you.
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Old 10-11-2011, 02:46 AM   #3
laura
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Our sequence data and all associated meta data is described in our sequence index file

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/sequence.index

This file is described in

ftp://ftp.1000genomes.ebi.ac.uk/vol1....sequence_data

The column you will be most interested in is 26 which describes the analysis group a run belongs to. All lanes labelled with exome are part of the exome sequencing project
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Old 10-11-2011, 06:43 AM   #4
efoss
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Thanks so much. That's exactly what I was looking for.

Eric
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