Problem with BED file in methylKit

bbm · 01-23-2017, 07:18 AM

Hello all!

I am using methylkit to analyze my methylation data in honey bees.
I have converted a reference genome annotation file (gff3 file) to a bed file, then I run

gene.obj=readTranscriptFeatures(system.file("extdata", "amel_OGSv3.2_sorted.bed",
package = "methylKit"))

The msg was that:
Calculating intron coordinates...
Error in convertBed2Introns(bed) : this is not a valid bed file.

My file is like this:
Group1.1 377 436 . . - amel_OGSv3.1 CDS 2 Parent=GB42164-RA
Group1.1 377 436 . . - amel_OGSv3.1 exon . Parent=GB42164-RA
Group1.1 377 79932 GB42164 0.786254 - amel_OGSv3.1 gene . ID=GB42164
Group1.1 377 79932 GB42164-RA 0.786254 - amel_OGSv3.1 mRNA . ID=GB42164-RA;Parent=GB42164
Group1.1 650 969 . . - amel_OGSv3.1 CDS 0 Parent=GB42164-RA

Should I only keep the first 3 required columns, and test it again?
Appreciate your thoughts.

Michael.Ante · 01-24-2017, 01:00 AM

Hi bbm,

I think the problem is not the name field, but the missing information on exon-intron structure (since the function "convertBed2Introns" called the error).
Parsing a GFF3 file into something well usable is always hard. I'd go for converting your gff3-file into a gtf file, which is then easier to convert to a bed-file with exon-intron information.

Cheers,

Michael

bbm · 01-24-2017, 07:30 PM

Thank you for your thoughts. I have downloaded a bed file of honey bee from UCSC and tested in R, but it's still not working. This bed file has all 12 columns.
The only difference is my bed file has "Group1" as the chromosome # in the first column, but the example file has "chr20" in the first column.

Error in convertBed2Introns(bed) : this is not a valid bed file

Quote:

Originally Posted by Michael.Ante

Hi bbm,

I think the problem is not the name field, but the missing information on exon-intron structure (since the function "convertBed2Introns" called the error).
Parsing a GFF3 file into something well usable is always hard. I'd go for converting your gff3-file into a gtf file, which is then easier to convert to a bed-file with exon-intron information.

Cheers,

Michael

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Combining fasta file and bed file into a different file using biopython,python	surachit	Introductions	0	10-25-2015 11:55 PM
Splitting a bed file in multiple bed files by track	albireo	Bioinformatics	3	12-18-2014 12:58 PM
Problem of methylKit: Too many false positive?	serenaliao	Epigenetics	2	05-06-2014 10:02 AM
Is there a BED file format validator? Does a BED file have to be sorted position?	LauraSmith	Bioinformatics	3	05-21-2013 12:54 PM
Qualimap problem with Region.bed file	AlliCox	Bioinformatics	1	04-16-2013 04:45 AM

01-23-2017, 07:18 AM	#1
bbm Member Location: North Carolina Join Date: Sep 2011 Posts: 38	Problem with BED file in methylKit Hello all! I am using methylkit to analyze my methylation data in honey bees. I have converted a reference genome annotation file (gff3 file) to a bed file, then I run gene.obj=readTranscriptFeatures(system.file("extdata", "amel_OGSv3.2_sorted.bed", package = "methylKit")) The msg was that: Calculating intron coordinates... Error in convertBed2Introns(bed) : this is not a valid bed file. My file is like this: Group1.1 377 436 . . - amel_OGSv3.1 CDS 2 Parent=GB42164-RA Group1.1 377 436 . . - amel_OGSv3.1 exon . Parent=GB42164-RA Group1.1 377 79932 GB42164 0.786254 - amel_OGSv3.1 gene . ID=GB42164 Group1.1 377 79932 GB42164-RA 0.786254 - amel_OGSv3.1 mRNA . ID=GB42164-RA;Parent=GB42164 Group1.1 650 969 . . - amel_OGSv3.1 CDS 0 Parent=GB42164-RA Should I only keep the first 3 required columns, and test it again? Appreciate your thoughts.

01-24-2017, 01:00 AM	#2
Michael.Ante Senior Member Location: Vienna Join Date: Oct 2011 Posts: 123	Hi bbm, I think the problem is not the name field, but the missing information on exon-intron structure (since the function "convertBed2Introns" called the error). Parsing a GFF3 file into something well usable is always hard. I'd go for converting your gff3-file into a gtf file, which is then easier to convert to a bed-file with exon-intron information. Cheers, Michael