[Trinity protocol] some question about step: quality assessment

[bongbimit]

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

http://trinityrnaseq.sourceforge.net..._tutorial.html

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

[westerman]

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.

[bongbimit]

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

[westerman]

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.

[bongbimit]

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