Thanks for the person telling me that there is a software called EMBLmyGFF3 that can convert gff3-like file into EMBL file. However, I applied the software to my fasta file and gff3 file, the result I got were all 'Gap's!!!? initially I thought it was because the source problem, which is stuff in third column in the gff file, after I changed and made It a second run, it made error again!!! do anyone have similar experience??? this stuff is driving me crazy....!
FT source 1..593586810
FT /mol_type="genomic DNA"
FT /organism="Wheat"
FT **gap** 4503..5478
FT /estimated_length=976
FT **gap** 11990..13040
FT /estimated_length=1051
FT **gap** 14847..14856
FT /estimated_length=10
FT **gap** 16648..16657
FT /estimated_length=10
FT **gap** 19956..24520
FT /estimated_length=4565
I don't see what's wrong with it .... Those gaps indicate gaps in your genomic sequence, and there likely be plenty of those indeed.
Scroll further downwards until you passed all these gaps tags and see what's printed there
Actually they. were all gaps. I wanted to transform my transposon element in GFF format to EMBL format, so the column which is displaying 'gap' now should be 'transposon', but I don't know why it failed.
strange, that makes very little sense ...
Can you post an extract of your GFF file so we can inspect?
sure.
Please use the formatting bar (especially the
code
option) to present your post better. I've done it for you this time.Thank you!
I don't understand...what's the difference ???:))
Using the code option converts text to monospace font. Without that option biostars code will try to interpret some symbols like
#
and change the formatting of text.okay, I got it. I will be careful to make it right next time.!!!
and the EMBLmyGFF3 cmdline ?
this gff file does already not correspond to the EMBL you have given previously.
it is like this:
I don't really know what these tag means, so I gave them by default.
If you don't care about the header and your downstream analysis focus only on the features (FT,SQ,etc...), you could keep fake/default information. Except maybe transl_table that could be important if you ask the tool to do the CDS translation and your species don't use the table 1...
Hello 3105298904 ,
have you tried to find your organism and gene on plants.ensembl.org? If you found your gene there you can export the data directly to EMBL format without any convertion.
fin swimmer
If I remember the original post, it thought it was to upload data to EBI/ENA