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sr320 / LabDocs

Roberts Lab Documents
http://sr320.github.io/LabDocs/
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Download SRA data #560

Closed sr320 closed 7 years ago

sr320 commented 7 years ago

Download C gigas SRA data that is methylation related- not from our own lab. Download to your directory in Scaphapoda

grace-ac commented 7 years ago

@seanb80 did it and showed me the process! thank you Sean!

Folder

kubu4 commented 7 years ago

It would be helpful if the process was detailed in your notebook.

seanb80 commented 7 years ago

http://rpubs.com/seanb80/267942 Grace gets to make the notebook post though!

kubu4 commented 7 years ago

@seanb80 - Why did you put this data on Eagle?

seanb80 commented 7 years ago

Because grace said to put it in her directory there.

On Apr 14, 2017, at 7:09 PM, kubu4 notifications@github.com wrote:

@seanb80 - Why did you put this data on Eagle?

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grace-ac commented 7 years ago

Because i was told to put it there :) On Fri, Apr 14, 2017 at 7:15 PM seanb80 notifications@github.com wrote:

Because grace said to put it in her directory there.

On Apr 14, 2017, at 7:09 PM, kubu4 notifications@github.com wrote:

@seanb80 - Why did you put this data on Eagle?

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kubu4 commented 7 years ago

On Eagle?

I believe you, but the reason I questioned it is Eagle hasn't been used for any active projects in a very long time (because it's nearly full, as @seanb80 noticed). So, I was surprised to see new data going there.

grace-ac commented 7 years ago

Yup! That's the only place I am aware of that has a folder of mine in scaphapoda! On Fri, Apr 14, 2017 at 7:19 PM kubu4 notifications@github.com wrote:

On Eagle?

I believe you, but the reason I questioned it is Eagle hasn't been used for any active projects in a very long time (because it's nearly full, as @seanb80 https://github.com/seanb80 noticed). So, I was surprised to see new data going there.

— You are receiving this because you were assigned.

Reply to this email directly, view it on GitHub https://github.com/sr320/LabDocs/issues/560#issuecomment-294266286, or mute the thread https://github.com/notifications/unsubscribe-auth/AOPhKl30Evoxgo0TedRiChlMLjCiJRv0ks5rwCkOgaJpZM4M0rrl .

sr320 commented 7 years ago

Grace said owl/scaphapoda is for newbs, she has legacy status:) On Fri, Apr 14, 2017 at 7:22 PM grace-ac notifications@github.com wrote:

Yup! That's the only place I am aware of that has a folder of mine in scaphapoda! On Fri, Apr 14, 2017 at 7:19 PM kubu4 notifications@github.com wrote:

On Eagle?

I believe you, but the reason I questioned it is Eagle hasn't been used for any active projects in a very long time (because it's nearly full, as @seanb80 https://github.com/seanb80 noticed). So, I was surprised to see new data going there.

— You are receiving this because you were assigned.

Reply to this email directly, view it on GitHub https://github.com/sr320/LabDocs/issues/560#issuecomment-294266286, or mute the thread < https://github.com/notifications/unsubscribe-auth/AOPhKl30Evoxgo0TedRiChlMLjCiJRv0ks5rwCkOgaJpZM4M0rrl

.

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yaaminiv commented 7 years ago

Just looking at the folder, there seems to be only one .fastq file (SRR5085013). Was there a problem downloading the other files?

grace-ac commented 7 years ago

@seanb80 ?

seanb80 commented 7 years ago

Hmm, there may have been! I will look in to it tomorrow morning. I tried to be clever and download then zip files to deal with the limited space, but that may not have worked.

On Tue, Apr 18, 2017 at 11:53 AM, grace-ac notifications@github.com wrote:

@seanb80 https://github.com/seanb80 ?

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yaaminiv commented 7 years ago

No worries! Also, I tried searching "SRR46473" in the SRA database but it said "No items found"...? I'm compiling all of the metadata for these runs.

grace-ac commented 7 years ago

I think it's supposed to be "SRR546473" https://www.ncbi.nlm.nih.gov/sra/SRX180561[accn]

grace-ac commented 7 years ago

I think these are the four data sets we were trying to download...? "SRR546473" is the second on the list. https://www.ncbi.nlm.nih.gov/sra?term=SRP015008

yaaminiv commented 7 years ago

script to download additional datasets: https://github.com/RobertsLab/paper-gigas-metaanalysis/blob/master/scripts/2017-19-04-Downloading-SRA-Data.R

kubu4 commented 7 years ago

@seanb80 - It might be a good idea to add an update to your original Rpub, so that someone doesn't stumble across it and try to use it.

seanb80 commented 7 years ago

I've tried to push an update a few times, but it doesn't seem to be properly updating at the page, will have to delete and re-upload I believe.

edit: Updated!