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Rfam / rfam-production

Rfam production pipeline
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Update microRNA families for release 14.7 #76

Closed AntonPetrov closed 2 years ago

AntonPetrov commented 3 years ago

The idea is to select microRNA families from the Family updates sheet of the microRNA dashboard (labelled Update in column N) and run the following steps to update them. I recommend starting with a handful of families and scale up to all once the scripts are working as expected.

  1. update_old_mirnas.py - check out the existing families with rfco.pl and copy over the new SEED alignments

  2. precompute.py - run rfsearch.pl to build a new covariance model (CM) and find the sequences matching it

  3. automake.py - run rfmake.pl with a manually selected threshold

  4. auto_addref.py - add miRBase reference to the DESC file

  5. A new step may be needed here to update various fields in the DESC file

    AU   Griffiths-Jones SR; 0000-0001-6043-807X
SE   Griffiths-Jones SR
SS   Predicted; RNAalifold

  6. auto_rqc.py - run rqc-all.pl to see if the family passes quality controls (QCs)

  7. run rfci.pl on the families that pass all QCs

emmaco commented 2 years ago

microRNA families have been updated for 14.7. We will continuing updating in future releases with the scripts in rfam-production/support/mirnas.