A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
I ran this with my gff3.gz but got a blank gtf file. The problem was fixed when I used gff3 file instead. I searched online that gffread may only take gff3 instead of gff3 compressed file. If true, could you fix your documentation?
Description of the bug
In the GEMmaker documentation, https://gemmaker.readthedocs.io/en/latest/prepare_reference.html#id3
singularity exec -B ${PWD} docker://systemsgenetics/gemmaker gffread Arabidopsis_thaliana.TAIR10.50.gff3.gz -T -o Arabidopsis_thaliana.TAIR10.gtfI ran this with my gff3.gz but got a blank gtf file. The problem was fixed when I used gff3 file instead. I searched online that gffread may only take gff3 instead of gff3 compressed file. If true, could you fix your documentation?
Best,
Command used and terminal output
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Relevant files
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System information
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