Alternate splicing-rMATS error

1

Hello all,

I am trying to analyze RNA-Seq data for alternate splice sites. I am using rMATS to do that but getting the following error:

File "RNASeq-MATS.py", line 231, in <module>
myLen=len(output.strip().split('t')[9]);
IndexError: list index out of range

what might be possibly wrong?

Thank You.


RNA-Seq


AlternativeSplicing


rMATS

• 3.2k views

hey, i bumped into this error now:

2016-08-17 14:45:59,543 rMATS version: 3.2.4
2016-08-17 14:45:59,543 Start the program with [RNASeq-MATS.py -s1 testData/231ESRP.25K.rep-1.R1.fastq:testData/231ESRP.25K.rep-1.R2.fastq,testData/231ESRP.25K.rep-2.R1.fastq:testData/231E$

2016-08-17 14:45:59,597 ################### folder names and associated input files #############
2016-08-17 14:45:59,598 SAMPLE_1REP_1  testData/231ESRP.25K.rep-1.R1.fastq:testData/231ESRP.25K.rep-1.R2.fastq
2016-08-17 14:45:59,598 SAMPLE_1REP_2  testData/231ESRP.25K.rep-2.R1.fastq:testData/231ESRP.25K.rep-2.R2.fastq
2016-08-17 14:45:59,598 SAMPLE_2REP_1  testData/231EV.25K.rep-1.R1.fastq:testData/231EV.25K.rep-1.R2.fastq
2016-08-17 14:45:59,599 SAMPLE_2REP_2  testData/231EV.25K.rep-2.R1.fastq:testData/231EV.25K.rep-2.R2.fastq
2016-08-17 14:45:59,599 #########################################################################

2016-08-17 14:45:59,599 start mapping..
2016-08-17 14:45:59,599 mapping the first sample
2016-08-17 14:45:59,611 mapping sample_1, rep_1 is done with status 26112
2016-08-17 14:45:59,612 error in mapping sample_1, rep_1: 26112
2016-08-17 14:45:59,612 error detail:
EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "alignEndsType" in input "Command-Line-Initial"
SOLUTION: use correct parameter name (check the manual)

Aug 17 14:45:59 ...... FATAL ERROR, exiting
2016-08-17 14:45:59,612 There is an exception in mapping
2016-08-17 14:45:59,612 Exception: <type 'exceptions.Exception'>
2016-08-17 14:45:59,612 Detail:


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