Help for coding: Trinity for differential gene expression studies

Question

[rhossen]

Hi, I am studying gene expression studies with 30 samples with trinity.

*I successfully completed abundance_estimation using:

--samples_file --est_method RSEM **--output_dir (in brief here).

Then I got the following output folders with RSEM results- Abl_1, Abl_2, Abl_3, Bn_1, Bn_2, Bn_3,... map,etc in my current working directory.

*Now I want to Build Transcript and Gene Expression Matrices by RSEM ~/abundance_estimates_to_matrix.pl --est_method RSEM --gene_trans_map** .... then what more options?

I want to use option to count my already created RSEM output as input here (--basedire may be), and I am bit confused about what more options I need to add in this command. The instruction in wiki is confusing to me for this section. Thank you for your time.

Answer 1

[mchour]

Hello, I would recommend following RSEM wiki for more information about the options, or even run RSEM directly, not with the script provided by Trinity.

[rhossen]

It should be great if I have any assistance in my build up command using trinity package...

[mchour]

This could help