SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Two-step PCR protocol for Illumina sequencing EmmaUoW Illumina/Solexa 2 08-30-2013 12:08 AM
question about the RSEM module within trinity ataraxia RNA Sequencing 0 08-20-2013 09:31 PM
Platform independent quality assessment of Exomes krawitz Bioinformatics 0 08-28-2012 02:04 AM
advice on the size selection step in ChIP-seq protocol mboth Sample Prep / Library Generation 5 10-13-2011 01:59 AM
ShortRead: a bioconductor package for input, quality assessment and exploration Chien-Yuan Chen Literature Watch 0 11-09-2009 01:36 PM

Reply
 
Thread Tools
Old 01-23-2014, 01:35 AM   #1
bongbimit
Member
 
Location: Ha Noi

Join Date: Dec 2013
Posts: 29
Default [Trinity protocol] some question about step: quality assessment

I have a question about the step " Quality assessment " in the Trinity protocol

After assembling all file .fq i have a file Trinity.fasta is the result. Next step is makeblastdb from a file name S_pombe_refTrans.fasta -> where is file come from ? Is S_pombe_refTrans.fasta Trinity.fasta ? because i know now i do denovo assembly without reference

Tks in advance
bongbimit is offline   Reply With Quote
Old 01-23-2014, 06:48 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

If you are asking "is the Trinity.fasta file the same as the S_pombe_refTrans.fasta file" then the answer is no.

I assuming that you are following the tutorial using the enclosed data and not just running Trinity on your own data set. When you untar the TrinityNatureProtocolTutorial.tgz file you should get both the raw reads files plus the S_pombe_refTrans.fasta. After running Trinity on the reads files you will get a Trinity.fasta file. Since we know that the reads come from S_pombe and since there is already a good reference for S_pomba then, as per the tutorial, it is feasible to compare the denovo assembly of the reads (e.g., Trinity.fasta) with what should be found.

If you are running Trinity on your own data set then, unless you are using reads from a well characterized species, then (as I would hope is obvious) there is no way to compare the denovo Trinity.fasta assembly to a known reference since the latter would not exist.
westerman is offline   Reply With Quote
Old 01-23-2014, 10:18 PM   #3
bongbimit
Member
 
Location: Ha Noi

Join Date: Dec 2013
Posts: 29
Default

Quote:
Originally Posted by westerman View Post
If you are asking "is the Trinity.fasta file the same as the S_pombe_refTrans.fasta file" then the answer is no.

I assuming that you are following the tutorial using the enclosed data and not just running Trinity on your own data set. When you untar the TrinityNatureProtocolTutorial.tgz file you should get both the raw reads files plus the S_pombe_refTrans.fasta. After running Trinity on the reads files you will get a Trinity.fasta file. Since we know that the reads come from S_pombe and since there is already a good reference for S_pomba then, as per the tutorial, it is feasible to compare the denovo assembly of the reads (e.g., Trinity.fasta) with what should be found.

If you are running Trinity on your own data set then, unless you are using reads from a well characterized species, then (as I would hope is obvious) there is no way to compare the denovo Trinity.fasta assembly to a known reference since the latter would not exist.
ok thank u for your help, it 's lucky if i have the reference genome ( or transciptome ) on my data set, but if i have i think i will not do trinity
bongbimit is offline   Reply With Quote
Old 01-24-2014, 07:28 AM   #4
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

Certainly if you have a known transcriptome then there is little reason to do a denovo transcriptome. There can be some case for which doing a denovo transcriptome could be useful but for a first-pass effort mapping to something known is better than trying to create your own.

I suggest Tophat & Cufflinks for transcriptome mapping however there are other programs as well.
westerman is offline   Reply With Quote
Old 01-24-2014, 05:57 PM   #5
bongbimit
Member
 
Location: Ha Noi

Join Date: Dec 2013
Posts: 29
Default

Quote:
Originally Posted by westerman View Post
Certainly if you have a known transcriptome then there is little reason to do a denovo transcriptome. There can be some case for which doing a denovo transcriptome could be useful but for a first-pass effort mapping to something known is better than trying to create your own.

I suggest Tophat & Cufflinks for transcriptome mapping however there are other programs as well.
Yes, the first protocol i read and try in rna-seq is Tophat and Cufflink but now my data set dont have a reference so i must denovo assembly by Trinity
bongbimit 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 05:51 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO