Converting TXT files into BED files

[Matteo Ruggiu]

Hello,

I would like to upload UV cross-linking and immunoprecipitation (CLIP) data onto the UCSC Genome Browser as custom tracks, but I am having some issues with the file format.

This is the source of the dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69710

In the link above I have a hard time locating the BED files. Under “Supplementary file”, I can download the zipped version of the TXT files. However, in order to upload them on the UCSC Genome Browser as custom tracks, I need to use BED files.

I’ve used BED files in the past as custom tracks, but in those cases I was able to download the BED files directly from the GEO website. In this case, it seems that only TXT files are available for download. However, TXT files are not accepted as data file formats on the UCSC Genome Browser.

I wonder if you can tell me how can I convert TXT files into BED files?

Thank you,

-- 

Matteo Ruggiu, PhD

Assistant Professor

St. John's University

Department of Biological Sciences

St. Albert Hall, Room 202
8000 Utopia Parkway,

Queens, NY  11439

Tel:   +1 718 990-5465

Fax:  +1 718 990-5958

rug...@stjohns.edu

Google Scholar: http://tinyurl.com/neg9m6n

[Chris Villarreal]

Dear Matteo,

Thank you for your question about the UCSC Genome Browser. At the
bottom of the link you provided there are supplementary data files in
BED format:

GSE69710_NOVA1_CLIP_clusters_BC2C10.bed.gz 122.9 Kb (ftp)(http) BED
GSE69710_NOVA2_CLIP_clusters_BC2C10.bed.gz 437.1 Kb (ftp)(http) BED

You can upload them into the browser via a custom track in two ways:

1. Download the files from the page and then upload them from your
computer into the Add custom tracks option.
Or
2. Right click on the link on the NIH page to copy it. Insert the link
into the "Paste URLs or data box" then give it a name. The format
should look like this:

track name=GSE69710_NOVA1_CLIP_clusters_BC2C10
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE69710&format=file&file=GSE69710%5FNOVA1%5FCLIP%5Fclusters%5FBC2C10%2Ebed%2Egz

The custom track loader will automatically fetch and decompress the data
from the URL, inserting it into the custom track.

I hope this is helpful. If you have any further questions, please reply
to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

-Chris V
UCSC Genome Browser

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