Recommended number of samples to use for trinity for DeSeq2

[Derek Benson]

Hi all,

I am constructing a reference transcriptome for differential expression using DeSeq2. I have 60 or so samples that I have prepped with rcorrector. When I try to run trinity with the 60 samples the runtime is estimated at 115 days. I am not sure what I am doing wrong. Previously I ran trinity with raw fastq files not prepped with rcorrector and it worked just fine. Is there something I can do to speed this process up, or is there a set number of samples you would recommend using when constructing a reference transcriptome?

Thanks in advance,

Derek

[Brian Haas]

Hi,

I'm not sure why it worked before and is not working well now post rcorrector. It's probably fine to just use the results from the job that succeeded earlier.  If you need to rerun, you could try adding --min_kmer_cov 2 (or 3), which should reduce the number of total read clusters.  When you have so much data, you likely don't need to work with the unique kmers.

hope this helps

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas