Index of /EvidentialGene/plants/arabidopsis
Name Last modified Size
Parent Directory 21-May-2017 19:09 -
evigene2017_arabidopsis/ 22-May-2017 20:28 -
evigene_tr2aacds_test/ 30-Oct-2021 20:59 -
evigene_tr2aacds_test2013/ 20-May-2013 13:16 -
evigene_tr2aacds_test2021/ 30-Oct-2021 20:59 -
Arabidopsis Gene Assembly from RNA-seq with EvidentialGene methods,
and comparison to Pac-Bio RNA, and genome modeled gene sets.
This is a reference-free gene set (no external data was used to make gene assemblies)
and has value for that (i.e. no errors from other sources complicate these genes).
Test case for EvidentialGene_trassembly_pipe (evigene/scripts/prot/tr2aacds.pl)
TEST RUN THIS outside of PBS/qsub cluster to see if it works:
env trset=arath_TAIR10_20101214up.cdna.gz datad=`pwd` ./tr2aacds_test.sh > & log.tr2ac1
NOTE: You need to edit the app paths in tr2aacds_test.sh for your system.
TEST DATA: arabidopsis TAIR10 transcripts (headers regularized, though probably not needed)
curl -sR -o arath_TAIR10_20101214up.cdna \
Get also TAIR10_pep and TAIR10_cds to compare w/ evigene output
This takes 20 min to run on 2 cores of intel game box