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hahnlab / CAGEE

Computational Analysis of Gene Expression Evolution
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Unknown option: replicate_map #23

Closed poojasingh09 closed 1 year ago

poojasingh09 commented 1 year ago

Hi, when I run cagee with a replicate_map I get the following error: cagee -c gene_oj.cfg
Unknown option: replicate_map

this is my gene_oj.cfg file contents:

Estimate a sigma2 for the given tree and gene transcripts with replicates

tree = RAxML_bipartitions.all.filt.L.vcf.SNP.gz.recode.mergedOnil.fmiss.raxmlout.T10.clean.CAGE.tre infile = gene_tpm_all_samples_onil_OJ.tsv replicate_map = replicate_map_oj.txt output_prefix = gene_oj

I installed cagee via conda and have v1.0; it seems v1.1 is not available via conda

cagee --version CAGEE 1.0

thanks,

pooja

benfulton commented 1 year ago

Replicate maps have not made it into any official release yet. You would have to download the source code and compile it yourself. Do you have a particular interest in this feature?

poojasingh09 commented 1 year ago

Hi Ben,

I have 5 biological replicates per species, so ideally I wanted to take that variation into account. Or should I just calculate the species mean across the replicates and use that for CAGEE?

I tried compiling it from source on a mac and got some errors; will try it again on our linux server.

thanks,

​Pooja

benfulton commented 1 year ago

Yes, calculating the species mean is probably the best idea for now. We'll do some more testing on the replicate model and hopefully get it into the next release.