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Old 10-30-2009, 10:17 AM   #3
Cole Trapnell
Senior Member
Location: Boston, MA

Join Date: Nov 2008
Posts: 212

Originally Posted by zslee View Post
has anyone here used tophat ?
when i map single-end solid sequences(fastq format) to hg18 as follow:
~/bin/tophat bowtie-0.11.3_index/hg18 query.fq -o mapre -a 5 -m 2 -i 70 -I 5000 --solexa1.3-quals -g 40 -p 4

there is such error:
Error: you must set the mean inner distance between mates with -r
Traceback (most recent call last):
File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1487, in ?
File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1402, in main
TypeError: 'str' object is not callable

what's going on ?
can anyone help me? thanks in advance~~
In the command above, you are placing the arguments (the index name and the FASTQ file of your reads) before the options. It should be:

tophat -o mapre -a 5 -m 2 -i 70 -I 5000 --solexa1.3-quals -g 40 -p 4 bowtie-0.11.3_index/hg18 query.fq
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