Question: Adding CDS features to Gff3 file
0
gravatar for abhijit.synl
21 months ago by
abhijit.synl50
United States
abhijit.synl50 wrote:

Hello,

I would like to add the CDS feature to my Gff3 file, that has exons in it. I saw that genometools can do this for you

gt cds -startcodon -finalstopcodon -seqfile foo.fasta -o foo.gff3 [GFF3-FILE]

I am looking for the CDS to be the longest ORF with an ATG start codon per mRNA. Will the above command give me that? Secondly I did not see a flag for specifying the genetic code. Is this by default "standard vertebrate"?

Thanks for the help Abhijit

ADD COMMENTlink modified 7 weeks ago by h.mon27k • written 21 months ago by abhijit.synl50

Though not directly but can be acheived using a combination of Genometools and PASA

ADD REPLYlink written 4 months ago by abhijit.synl50

This is resolved. please close thread

ADD REPLYlink written 4 months ago by abhijit.synl50

hi,i had the same problem recently, can you tell me the solution detail

ADD REPLYlink written 8 weeks ago by pigeon041110

thanks for your prompt reply, these help me a lot. but these still had a problem, after i processed the data accroding your method. the problem is : "gt cds: error file is not sorted." i think that may cause by absent some scaffold in my gff3 file, gt cds need all scaffold according to the order. gt cds will thought the file is not sorted, if some scaffold miss, even gff3 file had been sorted before. what's your opinion? thanks again!

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by pigeon041110

Please attach a sample of your Gff3 file. Maybe the first 250 lines.

ADD REPLYlink written 8 weeks ago by abhijit.synl50

i'm sorry i don't known how attach a file in this site, can you give me your email?

ADD REPLYlink written 8 weeks ago by pigeon041110

See this post on how to use GitHub Gist to share plain text files: A: How to Use Biostars Part-3: Formatting Text and Using GitHub Gists

ADD REPLYlink written 8 weeks ago by RamRS24k

abhijit.synl & pigeon0411 :

Please do not add answers unless you're answering the top level questions. You should have been using Add Comment and Add Reply appropriately.

I'm moving the extraneous "answers" to comments, but please be more careful in the future.

ADD REPLYlink written 8 weeks ago by RamRS24k
0
gravatar for abhijit.synl
8 weeks ago by
abhijit.synl50
United States
abhijit.synl50 wrote:

You will need to install the following and make sure they are in your PATH variable

1) Gffread utility 2) Genometools 3) GAAS Toolkit

a) Tidy your GFF3

gffread -C -F -T --no-pseudo -o FOO1".gtf" FOO.gff3
gt gtf_to_gff3 -tidy -force -o FOO".gff3" FOO1".gtf" (gt = GenomeTools executable)
gt gff3 -sort -tidy -retainids -addintrons -setsource "Genebank" -force -o FOO"_modi.gff3" FOO".gff3"

b) Keep Longest Isoform

gff3_sp_keep_longest_isoform.pl --gff FOO"_modi.gff3" --output FOO"_modi_longest.gff3" gff3_sp_keep_longest_isoform.pl = From GAAS Toolkit)

Hope this helps. This was a simpler solution than using PASA as mentioned in my previous post Abhijit

ADD COMMENTlink written 8 weeks ago by abhijit.synl50
0
gravatar for pigeon0411
7 weeks ago by
pigeon041110
China
pigeon041110 wrote:

hi,i find GAG-Genome Annotation Generator can add startcodon&stopcodon to gff file, thanks for everyone!

ADD COMMENTlink written 7 weeks ago by pigeon041110
0
gravatar for Juke-34
7 weeks ago by
Juke-342.6k
Sweden
Juke-342.6k wrote:

An easy way to do so would be to use TransDecoder

ADD COMMENTlink written 7 weeks ago by Juke-342.6k
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