Trinity Package

Question

[Varun Gupta]

Hi Everyone So i am actually working on Rna-seq data and i am interested in 80 Ribosomal protein genes. I am using this package called Trinity. Now this package has some command lines to run which includes some perl scripts. Since i am working on files with single end read, i would like to know that after i finish my trinity package how could i extract my 80 ribosomal protein genes of interest from that de novo built transcriptome.

It seems from the documentation that transcripts you get from trinity are very much self explanatory but have no gene names(or transcript names) and so how can i identify what are my transcripts of interest(in this case my 80 ribosomal proteins)

Any help would be appreciated

Thank You In advance

Regards Varun

Answer 1

[Rm]

Once you obtain the transcripts assembled; use them to blast/blat them against a sequence dataset (homologous genome or NT (which might includes 80 Ribosomal protein genes or their homologs).

Do you have reference genome sequence available for your sample? if so use tophat/cufflinks

[Varun Gupta]

Hi RM By transcripts assembled do you mean getting my Trinity.fa file. Because once i get my Trinity.fa file then i some how has to connect it to my ref genome seq(this is the fasta seq of my 80 ribosomal protein genes).

Yes i do have ref genome sequence which is fasta seq which i created for my 80 ribosomal protein genes . I also used tophat on it but some how the junctions.bed file produced is giving weird results. That is why i want to ask what to do using Trinity. Hope i explained myself better Any help would be appreciated Regards Varun