BED files

[Akhilesh Rawat]

Hi

Please let me know how to generate BED files with evenly padded both side of cosmic ID. I tried using Table browser but there option available are Whole gene, upstream and downstream only.

Please help

Thanks and Regards
Dr. Akhilesh Rawat, Ph.D.

Head R & D (Molecular Diagnostics)

3B BlackBio Biotech India Ltd.

7-C, Industrial Area, Govindpura, Bhopal-462023 [M.P.]

Phone :: +91-755-4077847

Fax :: +91-755-4282659

Mobile:: +91-8435593921

Website:: www.3bblackbio.com

Email:: rawat...@3bblackbio.com

[Matthew Speir]

Hello, Akhilesh.

Thank you for your question about the UCSC Genome Browser. 

Unfortunately, there is no option in the Table Browser to add padding bases both up and downstream at the same time. However, you can get basic BED output from the Table Browser and then use this little bit of awk code on the command line (e.g. Mac's terminal application) to add 100 bp of padding to the items in the BED file:

awk '{$2 -= 100; if ($2 < 0) {$2 = 0}  $3 += 100; print;}'  my.bed > my.padded.bed

In this command, "my.bed" is your output BED file from the Table Browser and "my.padded.bed" will be a file with the padding added to each BED item. If you would like to add more than 100 bp of padding then you would change the 100 in "$2 -= 100" and "$3 += 100" to whatever amount of padding you would like

I should also note that the data for the updated "COSMIC Regions" track available on the hg19 and hg38 human assemblies are not available from the Table Browser due to data distribution agreements with COSMIC. If you are not using this COSMIC Regions track, then it's likely you are using an outdated version of our now retired "COSMIC" track. From what I can tell, the data in this track was last updated in early 2015. If you'd like up-to-date data, then you can create an account and download it from the COSMIC website: https://cancer.sanger.ac.uk/cosmic. The file from COSMIC used to create the "COSMIC Regions" track in the UCSC Genome Browser is "CosmicMutantExport.tsv.gz".

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.

Matthew Speir

UCSC Genome Bioinformatics Group

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues?

Host a workshop: http://bit.ly/ucscTraining

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAAOjS__seQpSJ3b81U40whJ9%3DCSbiguyM%2BUhf2NUn4BkjZREoA%40mail.gmail.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.