convert GFF3 files from one genome version to another (Drosophila)

Question

[Biojl]

I'm trying to convert genomics coordinates that belong to peaks extracted from chip-seq experiments. The problem is that they were generated in version 5 of Drosophila melanogaster genome and we want to convert them to version 6. I know there is a web-tool in flybase: http://flybase.org/static_pages/downloads/COORD.html

But I was wondering if someone has a command line script or an alternative to ease our work, since we have to convert several files.

Thanks in advance

Answer 1

[Medhat]

CrossMap

Is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome. We do not recommend using CrossMap to convert genome coordinates between species.

[Biojl]

Thanks for the link! I can't find the liftover file for Dm5 to Dm6, it should be here, but it's not. http://hgdownload.soe.ucsc.edu/goldenPath/dm6/liftOver/

[Ryan Dale]

BDGP's Drosophila Release 5 is the same thing as UCSC's dm3. On this latest release, UCSC skipped dm4 and dm5 to use the name dm6 so that the assembly name matches the BDGP's Release 6. So the dm3 to dm6 chainfile is what you need.

[Medhat]

May be you can ask the flybase to support you with it

Answer 2

[Biojl]

I end up using a custom-modification of this script: https://github.com/FlyBase/bulkfile-scripts/blob/master/dmel_r5_to_r6/dmel_r5_to_r6_converter.pl