Thread: Tophat error
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Old 02-18-2019, 01:03 PM   #1
fanzhen
Junior Member
 
Location: USA

Join Date: Feb 2019
Posts: 2
Default Tophat error

I am new to RNAseq, I am trying to map my reads to my reference genome. It generates this error
Generating SAM header for /path/ref
Traceback (most recent call last):
File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 4107, in <module>
sys.exit(main())
File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 3961, in main
params.read_params = check_reads_format(params, reads_list)
File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 1856, in check_reads_format
zf = ZReader(f_name, params)
File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 1809, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: ''

Any ideas how to fix this?
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