GFF and Genome Fasta file
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Entering edit mode
8.8 years ago
aj123 ▴ 120

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

RNA-Seq gff fasta cuffdiff genome • 2.5k views
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Entering edit mode
8.8 years ago

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.

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

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