Big question - Transcriptome annotation

Dampor · 08-04-2014, 05:50 AM

Hi guys,

I have just finished to assemble my transcriptome ( I used Trinity, N50 is 2000, I am quite happy with it).
Now I would like to annotate it, particularly for doing some SNPs calling and want to know if they fall in CDSs or UTRs (I am using 6 populations, also looking for some good pipeline if you know one that uses transcriptomes).

I am aware of Trinotate, but is there something more "easy" or straightforward?

Cheers
Dam

colindaven · 08-04-2014, 06:17 AM

Perhaps Pedant is of interest ? http://pedant.gsf.de/

Otherwise, Blast2go is quite simple but in my experience not too great.

If you have a reference genome, perhaps map to that with gmap and use maker to annotate the whole thing.

Dampor · 08-04-2014, 06:23 AM

Tanks for the reply colindaven,

(forgot to mention) unfortunately there is no reference genome... therefore I need to get the transcriptome annotated as accurate as possible for the pop gen analyses

Cheers

frankM · 02-23-2015, 04:09 AM

You may want to use Annocript. It was just published on Bioinformatics and permits annotation of any type of transcriptome (both nucleotides and peptides). It is a pipeline that runs BLAST programs and gives the best HIT against SwissProt and TrEMBL or UniRef, CDD domains, rFam. Moreover it also presents which transcripts could be putative lncRNAs. It gives a lot of outputs: a complete table with the annotation, plots and statistics, blast output in GFF3 format, fasta file with the putative coding and long non coding sequences.

The program is straightforward to use and open source. Freely downloadable at:

github.com/frankMusacchia/Annocript

There you will also find some plugins to make differential expression analyses starting from a table with raw counts and the output of Annocript.

Dampor · 02-23-2015, 06:17 AM

Thanks Frank!

Although I have almost done with the analyses now, I'll have a look and keep in mind for the future

Cheers
D

kurban910 · 11-30-2015, 01:54 AM

hi @frankM and @Dampor
did you use Annocript for the annotaion of your transcriptome or some other tools? when you were doing annotaion did you use a server or just a PC would be fine? because i wanna annotate my assembled transcriptome file too. could you please tell me how you did that process?

sgoetz · 12-14-2015, 03:31 AM

Hi Kurban910.
Blast2GO should work fine for the functional annotation of an assembled transcriptome. The most time consuming step will be the blasting. You can do this locally and import the XMLs or at the NCBI. You can download Blast2GO here here and need to register for a free account here.

kurban910 · 01-02-2016, 04:25 AM

thanks @sgoetz
yeah, blast2go sure is a fine tool. finished the job already.

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08-04-2014, 05:50 AM	#1
Dampor Member Location: UK Join Date: Jun 2012 Posts: 14	Big question - Transcriptome annotation Hi guys, I have just finished to assemble my transcriptome ( I used Trinity, N50 is 2000, I am quite happy with it). Now I would like to annotate it, particularly for doing some SNPs calling and want to know if they fall in CDSs or UTRs (I am using 6 populations, also looking for some good pipeline if you know one that uses transcriptomes). I am aware of Trinotate, but is there something more "easy" or straightforward? Cheers Dam

11-30-2015, 01:54 AM	#6
kurban910 Member Location: urumqi Join Date: Jul 2014 Posts: 58	hi @frankM and @Dampor did you use Annocript for the annotaion of your transcriptome or some other tools? when you were doing annotaion did you use a server or just a PC would be fine? because i wanna annotate my assembled transcriptome file too. could you please tell me how you did that process? Last edited by kurban910; 11-30-2015 at 02:40 AM.

08-04-2014, 06:17 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	Perhaps Pedant is of interest ? http://pedant.gsf.de/ Otherwise, Blast2go is quite simple but in my experience not too great. If you have a reference genome, perhaps map to that with gmap and use maker to annotate the whole thing.

08-04-2014, 06:23 AM	#3
Dampor Member Location: UK Join Date: Jun 2012 Posts: 14	Tanks for the reply colindaven, (forgot to mention) unfortunately there is no reference genome... therefore I need to get the transcriptome annotated as accurate as possible for the pop gen analyses Cheers

02-23-2015, 04:09 AM	#4
frankM Junior Member Location: Italy Join Date: Feb 2015 Posts: 1	You may want to use Annocript. It was just published on Bioinformatics and permits annotation of any type of transcriptome (both nucleotides and peptides). It is a pipeline that runs BLAST programs and gives the best HIT against SwissProt and TrEMBL or UniRef, CDD domains, rFam. Moreover it also presents which transcripts could be putative lncRNAs. It gives a lot of outputs: a complete table with the annotation, plots and statistics, blast output in GFF3 format, fasta file with the putative coding and long non coding sequences. The program is straightforward to use and open source. Freely downloadable at: github.com/frankMusacchia/Annocript There you will also find some plugins to make differential expression analyses starting from a table with raw counts and the output of Annocript.

02-23-2015, 06:17 AM	#5
Dampor Member Location: UK Join Date: Jun 2012 Posts: 14	Thanks Frank! Although I have almost done with the analyses now, I'll have a look and keep in mind for the future Cheers D

12-14-2015, 03:31 AM	#7
sgoetz Member Location: Spain Join Date: May 2010 Posts: 11	Hi Kurban910. Blast2GO should work fine for the functional annotation of an assembled transcriptome. The most time consuming step will be the blasting. You can do this locally and import the XMLs or at the NCBI. You can download Blast2GO here here and need to register for a free account here.

01-02-2016, 04:25 AM	#8
kurban910 Member Location: urumqi Join Date: Jul 2014 Posts: 58	thanks @sgoetz yeah, blast2go sure is a fine tool. finished the job already.