I'm going through the RNAseq tutorial posted here:
Data upload and Fastqc goes well (nice job!); however, I run into a problem with the tophat step.
Tophat errors out with the paired end setting.
Using the reads in a single end mode works (I guess because the closure-search is irrelevant for SE reads)
An error occurred with this dataset:TopHat v2.0.9 tophat -p 4 -r 110 -a 8 -m 0 -i 70 -I 500000 -g 20 --library-type fr-unstranded --max-insertion-length 3 --max-deletion-length 3 --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --closure-search --min-closure-exon 50
Dataset 27: Tophat for Illumina on data 14 and data 19: accepted_hits
Tool execution generated the following error message:
Error in tophat: tophat: option --closure-search not recognized for detailed help see http://tophat.cbcb.umd.edu/manual.html