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Old 01-23-2011, 06:29 AM   #3
SongLi
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Location: Durham

Join Date: Oct 2010
Posts: 19
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Hi Simon,

Thank you for the reply.

The story is a bit compilcated.

1. I downloaded some colorspace data about a month back. Then I accidentally deleted the file, so I wanted to download again. However, I can only get reads in sequence space from the same place where I downloaded before.

for example, when I was trying to download the modEncode data for Drosophila from this link, I only get sequence space data.

http://trace.ncbi.nlm.nih.gov/Traces...m=search&s=seq

2. SRA tools do not work for me for some reason, I have a post before on this forum, and SRA tool was not terminating for a single color space file for about 24 hrs. I found the above link, from which I can download the data (which I wanted to download again now) from SRA. But now, it's not working again.

Any suggestion?
Thanks
Song Li


Quote:
Originally Posted by simonandrews View Post
You don't mention the specific sample you're interested in so it's difficult to give an exact answer. If the entry was deposited in base space then there won't be an option to download colorspace (since that wouldn't make any sense anyway).

If you have a .sra file instead of a direct fastq file then you can use the --dumpcs option to fastq-dump to get colorspace fastq files from the sra file.
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