pair end rna seq issue

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What steps will reproduce the problem?
1.run altanalyze to analyze pair-end rna seq data;
2.Seq was mapped with Tophat 1.4.1
3.Build Exon BED file from BAM with instructed command line
4. run altanalyze as instructed.

What is the expected output? What do you see instead?
altanalyze shd finish, but instead quit with following messages:
Processing exon/junction coordinates sequentially by chromosome...
* * * * * * * * * * * * * * * * * * * * * * user coordinates imported/processed
Importing read counts from coordinate data...
129485 junction read counts present for TopHat
Normalizing junction expression (RPKM analogue - 60nt length)... 13_exons.bed 
('chr1', 183074182, 183072530) v.2.0.6 test
Error Encountered... Exon or Junction of zero length encoutered... RPKM 
failed... Exiting AltAnalyze.
[1, 0, 60.0]
Traceback (most recent call last):
  File "AltAnalyze.py", line 4916, in AltAnalyzeSetup
  File "AltAnalyze.py", line 4374, in __init__
  File "AltAnalyze.py", line 5179, in AltAnalyzeMain
  File "RNASeq.pyc", line 1106, in alignExonsAndJunctionsToEnsembl
  File "RNASeq.pyc", line 616, in calculateRPKM
NameError: global name 'kill' is not defined

...exiting AltAnalyze due to unexpected error

What version of the product are you using? On what operating system?
v2.0.7 on windowns 64 system

Original issue reported on code.google.com by changx...@gmail.com on 6 Oct 2012 at 7:17

[GoogleCodeExporter]

Greetings,

Sorry about the problem. This bug had not come up in the past when testing for 
our different RNA-Seq test datasets, including paired ends, but I just 
replicated this error when a file naming issue (unmatchable junction and exon 
files). Can you email me you file names or take a screen shot of the directory 
that contains your junction/exon.bed files (nsalomonis@gmail.com)? If this is 
the case, I will try to develop some methods to detect and warn right when the 
analysis starts.

Original comment by nsalomo...@gmail.com on 8 Oct 2012 at 8:38

[GoogleCodeExporter]

i have the same error ,could you tell me how to fix the error ,thanks!!!

Original comment by zhiangr...@126.com on 9 Jan 2013 at 3:06

Attachments:

• error.jpg

[GoogleCodeExporter]

This problem is almost always caused due to an issue with how the exon and 
junction files are named. AltAnalyze must match up each exon and junction file 
that correspond to a single sample propperly, or this error will occur. An 
example of a valid pair of files names is "patient1__exon.bed" and 
"patient1__junction.bed". A bad example is "patient1_exon.bed" and 
"patient1_junction.bed", where only one and not two underscores are used. The 
text "exon" and "junction" here are not important (anything can be used 
following the __ and AltAnalyze automatically detects exon versus junction 
files based on the number of columns in the file). Rather, the identical sample 
name preceeding the double underscore must be present. In the next version of 
AltAnalyze (versoin 2.0.8), this problem will be caught before the analysis is 
run. 

Original comment by nsalomo...@gmail.com on 9 Jan 2013 at 5:04

• Changed state: Fixed