all my reads are 40bp single end reads.
it seems that there is something wrong with the junction mapping process
my tophat commands and error message are as follows
tophat --phred64-quals -o s_1_sequence ~/rd/work/rna_seq/genome_index/bowtie/mm9/mm9 s_1_sequence.txt
it seems that there is something wrong with the junction mapping process
my tophat commands and error message are as follows
tophat --phred64-quals -o s_1_sequence ~/rd/work/rna_seq/genome_index/bowtie/mm9/mm9 s_1_sequence.txt
[Sat Jun 4 01:11:54 2011] Searching for junctions via segment mapping
Warning: junction database is empty!
[Sat Jun 4 01:13:23 2011] Processing bowtie hits
Traceback (most recent call last):
File "/home/liuxq/mybin/tools/tophat", line 2584, in <module>
sys.exit(main())
File "/home/liuxq/mybin/tools/tophat", line 2543, in main
user_supplied_deletions)
File "/home/liuxq/mybin/tools/tophat", line 2376, in spliced_alignment
os.remove(unspl_bwtfile)
UnboundLocalError: local variable 'unspl_bwtfile' referenced before assignment
Warning: junction database is empty!
[Sat Jun 4 01:13:23 2011] Processing bowtie hits
Traceback (most recent call last):
File "/home/liuxq/mybin/tools/tophat", line 2584, in <module>
sys.exit(main())
File "/home/liuxq/mybin/tools/tophat", line 2543, in main
user_supplied_deletions)
File "/home/liuxq/mybin/tools/tophat", line 2376, in spliced_alignment
os.remove(unspl_bwtfile)
UnboundLocalError: local variable 'unspl_bwtfile' referenced before assignment
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