Problems with "sqanti-sim.py eval" and please update SQANTI-3

[SimonHegele]

Hi,

I ran into problems trying to evaluate both .gtf and .fasta- using any of the available alignment tools. I used the .gtf file provided in the mouse example as demonstrated in the tutorial and a .fasta-file that was generated by Rnabloom from long and short reads generated with SQANTI-SIM using the mouse example again.

1. GTF-file:
   cDNA_Cupcake crashes trying to read the file.

2. .fasta-file:
   a) minimap2:
   cDNA_Cupcake fails to convert the .sam files of minimap2 to .gff-files.
   This conversion step seems unnecessary since minimap is able to output .gff-files directly.
   b) gmap:
   SQANTI3 apparently needs an index which is not provided by SQANTI-SIM
   c) deSALT
   Same as for gmap
   c) uLTRA
   uLTRA itself crashes trying to align the transcripts

Log-files are attached to this issue.

As cDNA_Cupcake was dropped as a dependency in SQANTI3 v5.2.1 it might be worth considering to update SQANTI3 in SQANTI-SIM as well.

Best,
Simon

eval_fasta_deSALT.log
eval_fasta_gmap.log
eval_fasta_minimap2.log
eval_fasta_uLTRA.log
eval_gtf.log