I'm trying to analyze a single end dataset from SRA with the brand new version of TopHat (1.1). TopHat crashes with the below error message, and looking at this & the code it appears that even with single ends it is trying to run a validation check on the 2nd set of reads
If I replace line 2093 with
Then I get farther but hit a new error
I'm too worn out to puzzle how to get past that one -- my best guess is this is related to the "extra" colorspace value which bowtie option "--col-keepends" deals with
Code:
File "/usr/local/bin/tophat", line 2093, in main params.read_params = check_reads(params.read_params, left_reads_list + "," + right_reads_list) TypeError: cannot concatenate 'str' and 'NoneType' objects
If I replace line 2093 with
Code:
if params.skip_check_reads == False: if right_reads_list !=None: params.read_params = check_reads(params.read_params, left_reads_list + "," + right_reads_list) else: params.read_params = check_reads(params.read_params, left_reads_list)
Code:
Length mismatch between sequence and quality strings for SRR040290.1 VAB_ugc_85__100_137__138_121__123_bc_Frag50_solid0032_20090715_ugc_121__1231_49_36 length=50 (51 vs 51).
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