SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Is it possible to convert a SNP.txt to a bed file or get a SNP.bed from samtools? Ling Bioinformatics 7 04-02-2015 06:17 AM
Updated How to convert .txt file to .bed .GFF or .BAR file format, forevermark4 Bioinformatics 2 06-30-2014 05:02 AM
TopHat file.bam file.bed join Trudy Bioinformatics 1 05-21-2013 11:59 AM
Is there a BED file format validator? Does a BED file have to be sorted position? LauraSmith Bioinformatics 3 05-21-2013 11:54 AM
Converting Dindel VCF file to GATK BED file MolecularToast Bioinformatics 2 09-24-2011 06:38 PM

Reply
 
Thread Tools
Old 10-13-2010, 09:01 AM   #1
joseph
Member
 
Location: ca

Join Date: Feb 2008
Posts: 39
Default bed file around the TSSs

Hi
I would highly appreciate if you could show me how to create a bed file around the TSSs from UCSC databases such as ensembl or refSeq genes. I need 350 nucleotides upstream and 150 nucleotides downstream of TSSs. The bed file should look like below, where:
Code:
chromStart is 350 nucleotides upstream of TSS
chromEnd is 150 nucleotides downstream of TSS
name is Name of gene or transcript_id depending on the database.

chrom	chromStart	chromEnd	name		score	strand
chr1	67051159	67163158	NM_024763	0	-	
chr1	67075869	67163158	NM_207014	0	+	
chr1	16762998	16812569	NM_017940	0	-
Thanks
Joseph
joseph is offline   Reply With Quote
Old 10-13-2010, 10:10 AM   #2
malachig
Senior Member
 
Location: WashU

Join Date: Aug 2010
Posts: 117
Default

Have you considered using the EnsEMBL API for these kinds of tasks?

Ensembl API docs
malachig is offline   Reply With Quote
Old 10-13-2010, 11:32 AM   #3
adamdeluca
Member
 
Location: Iowa City, IA

Join Date: Jul 2010
Posts: 95
Default

On the UCSC table browser go to the "Genes and Gene Predictions" group, select the table you want (ensGene, refGene, etc). Change the output format to "Selected fields..." and on the next page select the chr and the TSS. You can then pad the TSS by doing something like:
Code:
awk '{print $1"\t"$2-349"\t"$2+350}' file > TSS.bed
adamdeluca is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:15 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO