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
Converting Dindel VCF file to GATK BED file MolecularToast Bioinformatics 2 09-24-2011 06:38 PM
How to convert eland file to BED format huo Bioinformatics 1 01-19-2011 10:43 AM

Reply
 
Thread Tools
Old 02-15-2012, 09:35 AM   #1
LauraSmith
Junior Member
 
Location: SAN FRANCISCO

Join Date: Dec 2011
Posts: 4
Post Is there a BED file format validator? Does a BED file have to be sorted position?

Hi Everyone,

I have 2 questions and would very much appreciate anyone's input:

1. Is there a BED file format validator? A tool or a java package perhaps available online to download?


2. Does a BED file have to be sorted by chromosome and position starting from the first line? I checked the UCSC Genomic browser website for BED file format specification and there doesn't seem to be a requirement for this, but wanted to double check here.

Thank you,
Laura
LauraSmith is offline   Reply With Quote
Old 02-16-2012, 06:19 AM   #2
mgogol
Senior Member
 
Location: Kansas City

Join Date: Mar 2008
Posts: 197
Default

1) Not that I know of. Try to upload it to UCSC?

2) No. Unless you're trying to do something with it that expects it to be sorted. If you need to sort, something like sort -k1,1 -k2,2n file.bed should do.
mgogol is offline   Reply With Quote
Old 02-23-2012, 01:59 AM   #3
maasha
Senior Member
 
Location: Denmark

Join Date: Apr 2009
Posts: 153
Default

Using read_bed from Biopieces (www.biopieces.org) there is a -C switch that checks integrity:

http://code.google.com/p/biopieces/wiki/read_bed
maasha is offline   Reply With Quote
Old 05-21-2013, 11:54 AM   #4
AlexReynolds
Member
 
Location: Seattle, WA

Join Date: Feb 2013
Posts: 45
Default

If you want to validate coordinates, the BEDOPS bedops application can do this, using the --everything and --ec operators:

$ bedops --ec --everything myData.bed 1> /dev/null
...


If any problems with chromosome name or coordinates are found, the details will be printed to standard error; in this example, we direct standard output to /dev/null as we're only interested in finding and reporting errors.

Last edited by AlexReynolds; 05-22-2013 at 06:32 PM.
AlexReynolds is offline   Reply With Quote
Reply

Tags
bed file format

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 08:40 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO