The difference between stitcher.py and ss3iso.py

[lamyankin]

Hi,
Thank you for your efforts in this paper. But I'm a little confused about the step2 and step4 in the smart-seq3 repository.

1. The step 2 stitcher.py is used to reconstrut the RNA molecule, the step4 as well. What is the difference between them?
2. If every reads in the input file of step4 the ss3iso.py should have a UB:Z tag, should I filter the reads in the bam file from zUMIs pipline because the bam file includes the Internal reads which have not UB:Z tag.

Looking forward to your reply.

[cziegenhain]

Hi,

1.Stitcher can be used to assemble the actual sequence of the reconstructed molecule, whereas step 4 just uses the information per molecule to try to assign to is-forms.
2.Internal reads still have a UB tag but the value will be empty.