SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNAseq: Pipeline to detect allele specific expression dariober Bioinformatics 9 07-17-2015 01:46 PM
who coined RNAseq? RNAseq as an alignment first approach only brachysclereid Bioinformatics 3 01-10-2012 01:17 PM
ChIP-Seq: Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq dat Newsbot! Literature Watch 0 10-08-2011 03:40 AM
ERANGE-RNASeq with ensemble annotation Matthias Bioinformatics 0 02-23-2011 06:05 AM
What is the best pipeline for RNASeq atm? foxyg Bioinformatics 6 09-02-2010 08:56 PM

Reply
 
Thread Tools
Old 12-15-2010, 09:51 AM   #1
vebaev
Senior Res.
 
Location: Plovdiv, Bulgaria

Join Date: Oct 2008
Posts: 110
Default plant annotation pipeline for assembled RNAseq?

Dear all,
since I'm not deeply into protein-coding genes I wanted to ask If I have already huge number of assembled RNA sequences (EST) from illumina is there a piplines for automatic annotation of sequences based on homology (for example to Arabidopsis proteins with blastX) or I should write my oun script?


Thanks

PS
the new seqs from illumina are plant with non-sequenced genome
vebaev is offline   Reply With Quote
Old 12-15-2010, 01:11 PM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

blast2go is one solution.
westerman is offline   Reply With Quote
Old 12-16-2010, 07:20 AM   #3
vebaev
Senior Res.
 
Location: Plovdiv, Bulgaria

Join Date: Oct 2008
Posts: 110
Default

Thanks it looks very interesting!
vebaev is offline   Reply With Quote
Old 03-25-2011, 07:21 AM   #4
sarwar
Member
 
Location: delhi , india

Join Date: Apr 2010
Posts: 14
Default

Hey vebaev ! Now a days i am also in the same situation where i have analyse and annotate the assembled RNA sequences. So what strategies you used that with your case. Can you please give the detail or refer any paper or pipeline which is standard in scientific community to annotae characterise transcriptome assembly. OF course mine organism is non model plant organism.

Thanks in advance
sarwar is offline   Reply With Quote
Old 03-25-2011, 08:23 AM   #5
vebaev
Senior Res.
 
Location: Plovdiv, Bulgaria

Join Date: Oct 2008
Posts: 110
Default

Hi,
I used blast2go it is quite cute program...
vebaev is offline   Reply With Quote
Old 03-25-2011, 08:44 AM   #6
usad
Member
 
Location: aachen

Join Date: Sep 2009
Posts: 53
Default Plant classification pipeline

Hi,

You might want to try our Mercator Plant classification pipeline. It will also create some kind of annotation.

http://mapman.gabipd.org/web/guest/mercator.


Cheers,
bj
usad is offline   Reply With Quote
Old 04-18-2011, 07:04 PM   #7
blindtiger454
Member
 
Location: Omaha, NE

Join Date: Oct 2010
Posts: 30
Default

I suggest you use the NCBI protein database first. We did plant transcriptome assembly and a small percent (~5%) of our assembled and annotated transcripts were contaminants, such as bacterial, viral, and fungal sequences. Probably metagenomic leftovers, but the only way to catch them is to use the NCBI NR database, and look at the taxonomy of each best blast hit. If you use a plant database only, some of the contaminant sequences will match a plant protein will some similarity, and will be annotated as such. Then when RNA-Seq analysis is performed, I've seen instances where these contaminant sequences will show significant differential expression if they are not removed from your dataset.
blindtiger454 is offline   Reply With Quote
Old 04-18-2011, 08:13 PM   #8
sarwar
Member
 
Location: delhi , india

Join Date: Apr 2010
Posts: 14
Default

But again i would like to advice about parameter of similarity , we generally take E-value <1e-10 and alignment length 100 and identity more than 80% . If you have chosen same or similar and then giving 5% contaminants , we have to be careful.
sarwar is offline   Reply With Quote
Old 06-22-2011, 09:19 AM   #9
shengandy
Junior Member
 
Location: CT, USA

Join Date: Jun 2011
Posts: 3
Default

I am in similar situation. Working with non-model species with RNA-seq results. I am using blast2go for annotation. It is time-consuming considering about the data of RNA-seq. Is there any alternative? Thanks, SH
shengandy is offline   Reply With Quote
Old 06-23-2011, 02:49 AM   #10
usad
Member
 
Location: aachen

Join Date: Sep 2009
Posts: 53
Default

Dear shengandy

If you really were only interested in speed you could use simple blast (with a sprinkle of reciprocal best blast) versus a related (and well annotated) species . I would not really recommend it though, usually spending more time to get something decent always pays of.

And usually all the annotation pipelines don't take that long if you have some decent infrastructure. (If not maybe you get in touch with some local groups?)

Cheers,
Bj
usad is offline   Reply With Quote
Old 06-23-2011, 07:00 AM   #11
shengandy
Junior Member
 
Location: CT, USA

Join Date: Jun 2011
Posts: 3
Default

Dear Usad,

Thanks for your response. I do care about the quality. That is why I did not choose to blast against certain genome. I have about 2 million sequences from de novo assembly. It will take about 20 days if everything goes well and it won't use up the memory. Is this the general situation for annotation? Thanks -SH
shengandy is offline   Reply With Quote
Old 06-25-2011, 05:27 AM   #12
Tanushree
Junior Member
 
Location: Ahemdabad

Join Date: Mar 2011
Posts: 9
Default

hello!!
i am trying to install maker software but it has large number of dependencies , can any one help me with that. or suggest any other tools which can identify transposons , SSRs and other gene features.
Tanushree is offline   Reply With Quote
Old 06-25-2011, 08:56 AM   #13
DZhang
Senior Member
 
Location: East Coast, US

Join Date: Jun 2010
Posts: 177
Default

Hi,

I use both blast2go and nr blastx to annotate RNA seq data. One thing I would like to share is that blastx as standalone or via blast2go takes a huge amount of time if you use NCBI/EBI due to load restriction. So if you need quick results, you definitely seek other resources for blast/interproscan. Also install the GO database locally can dramatically improve the speed, too.

Best regards,
Douglas
www.contigexpress.com
DZhang is offline   Reply With Quote
Old 06-07-2014, 01:28 PM   #14
kashif_nawaz
Junior Member
 
Location: New Delhi

Join Date: Jun 2014
Posts: 6
Default

Hi..
I have a list of genes from cufflinks from one organism (Oryza sativa indica). All gene are important to be functionally categorize. I want to do GO and other same stuff from blast2go. How can I do it? Or can I use any other fast technique other than blast2go? Please suggest me
kashif_nawaz is offline   Reply With Quote
Old 06-07-2014, 01:59 PM   #15
sarwar
Member
 
Location: delhi , india

Join Date: Apr 2010
Posts: 14
Default

your question is not clear to me. if you want to do with blast2go, you please install and give your genes as input and then find out go terms, using first blast tab and then map and annotaion . However, there is another quick way to map to go terms if your genes are mapped to uniprot gene id. if you have gene id from uniprot or simply map to uniprot genes and get id. go to retrieve tab of uniprot , upload the id and you will get all go terms as well as go slim of all the genes.
sarwar is offline   Reply With Quote
Old 06-08-2014, 01:28 AM   #16
kashif_nawaz
Junior Member
 
Location: New Delhi

Join Date: Jun 2014
Posts: 6
Default

Hello Mr. Sarwar
thanks for replying. I have installed the blast2go already, but in blast2go as I know one has to blast the list of sequences in fasta format then we can do the GO. I have a list of genes which are expressed in a rice variety I want to functionally categorize that gene without blast. Is it possible without blast?
And Thanks for UniProt Suggestion.
kashif_nawaz is offline   Reply With Quote
Old 06-08-2014, 02:06 AM   #17
sarwar
Member
 
Location: delhi , india

Join Date: Apr 2010
Posts: 14
Default

Balst is actually to assign the function of the gene. the idea is to transfer the function of annotated gene to the query gene on the basis of similarity.
sarwar is offline   Reply With Quote
Old 06-08-2014, 02:17 AM   #18
kashif_nawaz
Junior Member
 
Location: New Delhi

Join Date: Jun 2014
Posts: 6
Default

Thank you Mr Sarvar
In uniprot retrieval process they are asking the gene in the uniprot ID but I have the genes in the BGI (Beijing Genomics Institute) ID form. Can you suggest me how to convert this bgi to uniprot id.
kashif_nawaz is offline   Reply With Quote
Old 06-08-2014, 02:28 AM   #19
sarwar
Member
 
Location: delhi , india

Join Date: Apr 2010
Posts: 14
Default

How many genes you have. if number is less blast in uniprot (i dont think uniprot take in batch so one by one). Otherwise download uniref90 and blast with it on fairly stringent criteria. Take the id of best hit for each protein.
sarwar is offline   Reply With Quote
Old 06-08-2014, 02:37 AM   #20
kashif_nawaz
Junior Member
 
Location: New Delhi

Join Date: Jun 2014
Posts: 6
Default

I have 24175 gene list but i dont have the sequence of those genes. The only thing I have is its BGI ID, I dont have any other ID like uniprot or ncbi.
Ex.
BGIOSGA002569
BGIOSGA002571
BGIOSGA002572
BGIOSGA002567
BGIOSGA002570
BGIOSGA002566
BGIOSGA002582
BGIOSGA002581
BGIOSGA002587
BGIOSGA002579
BGIOSGA002573
BGIOSGA002564
BGIOSGA002574
These are few examples. All these genes are from a rice species only (Oryza sativa indica). I want to categorizes these genes on the basis of there function?
Please help..
kashif_nawaz is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:15 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO