Creating a Trinity assembly

Question

[langziv]

Hi.
The data I got was obtained from an experiment with the following structure:
3 similar experiments in separate dates, each included a control group and an experiment group.
Should I create an assembly for each date, or should I create one assembly for data from all 3 dates?

Answer 1

[GenoMax]

If the aim is to create a comprehensive transcriptome first then create an assembly from entire dataset.

[langziv]

Thanks for the reply. From your answer I understand that you suggest creating a single assembly, rather than multiple. How should the assembly be created? from which RNA-seq fastq file? I didn't see an option to create an assembly from multiple fastq files.

[biofalconch]

You can do an assembly from multiple files, taken from the tool's help:

#  If paired reads:
 #      --left  <string>    :left reads, one or more file names (separated by commas, not spaces)
 #      --right <string>    :right reads, one or more file names (separated by commas, not spaces)
 #
 #  Or, if unpaired reads:
 #      --single <string>   :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: --run_as_paired )
 #

So basically just put the names separated by commas after the parameters and should be fine.

[langziv]

I was directed in the Trinity Google group to use the --samples_file parameter. If I understand correctly, both options get the same result.

[biofalconch]

That is correct, and my guess that this is helpful in the downstream analyses like the use of align_and_estimate_abundance.pl from the utils in the Trinity package