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Old 01-22-2011, 01:03 PM   #1
SongLi
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Default Download from SRA archive

Hi,

I recently tried to download published Colorspace results from SRA archive. http://www.ncbi.nlm.nih.gov/sra

However, I could only download sequences in ATCG. About one month back, I downloaded some colorspace data, which are in 0123 format.

Where can I download reads in colorspace from SRA?

Thanks,
Song Li

Last edited by SongLi; 01-22-2011 at 01:06 PM.
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Old 01-23-2011, 02:08 AM   #2
simonandrews
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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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Old 01-23-2011, 06:29 AM   #3
SongLi
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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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Old 01-23-2011, 11:45 PM   #4
simonandrews
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Quote:
Originally Posted by SongLi View Post
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
There is indeed something odd about that entry. Even if you set the display preferences to show colorspace (and colorspace data shows up in the preview view), then you still seem to get base space when you download the fastq file. In this case it may be that the only way to get the colorspace data is from the sra file (which I agree is a pain).

It might be worth contacting NCBI since this could just be a bug in their download code.
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Old 04-22-2011, 09:55 AM   #5
mjpablo23
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Default found the files?

Hi,
Were you able to download the colorspace files? I've been looking for them too.
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