Question: How to combining the RNA-seq data from different tissues of one individuals plant
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gravatar for yahalashinnosuke
4 days ago by
yahalashinnosuke0 wrote:

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!

rna-seq • 82 views
ADD COMMENTlink modified 4 days ago by lieven.sterck9.4k • written 4 days ago by yahalashinnosuke0
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gravatar for lieven.sterck
4 days ago by
lieven.sterck9.4k
VIB, Ghent, Belgium
lieven.sterck9.4k wrote:

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)

ADD COMMENTlink written 4 days ago by lieven.sterck9.4k

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!!!

ADD REPLYlink written 4 days ago by yahalashinnosuke0

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.

ADD REPLYlink written 4 days ago by GenoMax94k

Thank you!! It's very helpful!

ADD REPLYlink written 1 day ago by yahalashinnosuke0
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