GFF and Genome Fasta file

Question

[aj123]

Hello,

Please let me know if the gff and genome fasta file have to be the same when running a cuffdiff analysis. for example,

can I use these:

For the genome version: ftp://ftp.ensemblgenomes.org/pub/release-28/plants/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.28.dna.toplevel.fa.gz

For the gff files:

Please note that chromosomes are labeled as 'ChrX', while the fasta is labeled as 'X' ftp://ftp.arabidopsis.org/Maps/gbrowse_data/TAIR10/TAIR10_GFF3_genes_transposons.gff

Answer 1

[Joseph Pearson]

Yes, the chromosome names must be exact matches (unless things have changed recently), so having "ChrX" vs "X" in different files will be an issue.

The *nix command-line utility sed would be the best option, and it would be simpler (fewer changes) to change the fasta file chromosome names to match the gff names.

[aj123]

yes, thanks sed and awk seem to work best in such cases!