Question about REDItools

Question

[tujuchuanli]

Hi,

I wanted to use REDItools to identify RNA editing events in my data. I had both RNA-seq and exome-seq data derived from the same sample.

I download the latest version of REDItools (REDItools-1.2.1.zip, https://sourceforge.net/projects/reditools/files/) and test data (http://srv00.recas.ba.infn.it/reditools/data/testREDItools.tar.gz).

When I run the scripts “REDItoolDnaRna.py” as “REDItoolDnaRna.py -i rna.bam -j dna.bam -f reference.fa -o reditool-test -c 10,1 -q 25,25 -m 20,20 -s 2 -g 1 -u -a 6-0 -v 2 -n0.0 -N0.0 -V” basically following the README in test data folder to test the running. It returned err message as following:

Pysam version used: 0.15.3

Script time --> START: 02/09/2019 23:18:36

Analysis ID: 464424299

Analysis on 1 regions.

Started analysis on region: chr21:1-48129895

Process Process-1:

Traceback (most recent call last):

File "/usr/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run()

File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(self._args, *self._kwargs)

File "REDItoolDnaRna.py", line 1177, in do_work exploreBAM(x)

File "REDItoolDnaRna.py", line 1121, in exploreBAM seq,qual,squal=normByStrand(seq,strand,squal,mystrand)

File "REDItoolDnaRna.py", line 621, in normByStrand if type(i)==int: qual+=ord(squal_[str(i)])-QVAL

TypeError: list indices must be integers, not str

Merging Tables.

Results saved on reditool-test/DnaRna_464424299/outTable_464424299

Script time --> END: 02/09/2019 23:18:38

Then I found that it could be no err message returned when I deleted “-s 2” from the command line. However, the output file could be empty this time.

Could you help me? Thanks.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[Ethan Lee]

Excuse me, recently I've had the exactly same problem as you had 4 years ago......Could you please tell me how you dealt with it before, if you still remember? It would be very helpful to me! Thanks a lot!