Question: GFF and Genome Fasta file
0
gravatar for aj123
3.9 years ago by
aj12380
United States
aj12380 wrote:

 

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 cuffdiff gff genome fasta • 1.4k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by aj12380

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

ADD REPLYlink written 3.9 years ago by aj12380
1
gravatar for Joseph Pearson
3.9 years ago by
UNC Chapel Hill
Joseph Pearson450 wrote:

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.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Joseph Pearson450

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

ADD REPLYlink written 3.9 years ago by aj12380
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