evolinc-ii's People
evolinc-ii's Issues
please add the option for multiple processes when running the blastn
I notice that the EvoLinc-2 only use 4 thread. But Our server cluster have more than 128 thread per node. And, my task, even one ninght passed, didn't done just one species. We have 18 species together. I cann't image how long it will take. Please tell me how to set the multiple threading or multiple processes. Thank you a lot!
Replace BLAST with LAST to improve performance.
Scan through sequence homologs for coding potential
It would be nice to screen through all identified sequence homologs (the ones that don't have any annotation) with Evolinc-I to see if they are also putative lncRNAs.
Bed file is perceived as a quant file by CoGe
Need to modify the code to make the bed file a gff instead (perhaps a CoGe-specific issue).
Replace underscores in FASTA headers with "."
Create "intronic space" parameter
Allow for variable distance for removing gaps and merging hits on similar scaffolds (max gap length currently set to length of query lncRNA).
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