Failing trypsin digestion

[gwajnberg]

This is the output:

NovelJunc-chr14-106175001-106331409|chr=14|type=novel|site1=106175001|site2=106331409|reads=74|frame=1-
WYFDLWGRGTLVTVSSASPTSPKVFPLSLCSTQ

where this sequence should be cleaved in three :
WYFDLWGR = GTLVTVSSASPTSPK=VFPLSLCSTQ

I tried using with and without --no_missed_cleveage

those were teh parameters : quilts.py --output_dir --genome --proteome --somatic -- germline --junction --junction_file_type star [--no_missed_clevage]

[ekawaler]

When there is a proline on the C-term side of a K/R trypsin will not cleave. Also, make sure you spell the parameter correctly (--no_missed_cleavage)

[gwajnberg]

sorry i didn't misspelled in the command line !

I was trying to modify the code the trypsinize function, but I am still getting the same result .

in the condition of line 1048 I removed the " and next_letter != P"