Question: issues with GTEx data annotation files
0
gravatar for david.peeney
3 months ago by
david.peeney20
david.peeney20 wrote:

Hi all... I am having issues with obtaining sample annotation data from the GTEx dataset, specifically the origin tissue (which should be under the column "SMTSD". Spaces are used as a delimiter in the dataset, but I cannot get the data to appropriately align in excel (probably because some data points are blank).

Has anyone else had this issue and can people help.

The link to the data is below:

https://storage.googleapis.com/gtex_analysis_v7/annotations/GTEx_v7_Annotations_SampleAttributesDS.txt

Thanks!

gtex excel • 220 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by david.peeney20

The file is tab delimited, go check your excel Data -> Text to Columns

ADD REPLYlink modified 3 months ago • written 3 months ago by magicpants60

I have tried it... For some reason excel is not recognizing the tabs. Maybe I will try excel on a windows machine

ADD REPLYlink written 3 months ago by david.peeney20

same problem on windows. If anybody else can successfully perform the text to columns function, please let me know

ADD REPLYlink written 3 months ago by david.peeney20

No problem when I open this kind of text file in Mac excel, how did you open that? Or you can just use unix command line like cut to extract the columns and annotate files.

ADD REPLYlink written 3 months ago by magicpants60
1
gravatar for david.peeney
3 months ago by
david.peeney20
david.peeney20 wrote:

Ok... was actually really simple. Although it never worked as a text file in excel, i converted the file to .csv in R.

ADD COMMENTlink written 3 months ago by david.peeney20
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