How to combining the RNA-seq data from different tissues of one individuals plant

Question

[yahalashinnosuke]

I have RNA-seq data from different tissues of one individuals. I wonder how to combine all these RNA-seq data from different tissues and then used it as a single input for assembly. The aim is to get as many expressed genes as possible. Thank you!

Answer 1

[lieven.sterck]

Blunt approach: throw all your RNAseq data together and assemble as it were one big dataset/project.

alternatively (but considerable more work) is to first assemble RNAseq data per tissue and then combine all the different assemblies together (and in remove redundancy). This way you will have a higher chance of identifying tissue specific genes/isoforms , downside is that you might loose some genes due to not enough coverage of them in each of the samples (will you might have enough coverage when you use all RNAseq data from all tissues)

[yahalashinnosuke]

Thank you for your advice! However, I want to know how to throw all RNAseq data together? Any software can do this? If you could recommond certain software or pipeline, it would be very helpful!! Thank you!!!

[GenoMax]

trinity (LINK) is the go to software for eukaryotic transcriptome assemblies. You would basically use all of your data as input for a trinity run.

Trinity --seqType fq --max_memory 50G  \
         --left condA_1.fq.gz,condB_1.fq.gz,condC_1.fq.gz \
         --right condA_2.fq.gz,condB_2.fq.gz,condC_2.fq.gz \
         --CPU 6

Please pay attention to memory (and other) requirements for trinity.

[yahalashinnosuke]

Thank you!! It's very helpful!