I tried to run tophat a lot and I haven't success. I need help please!!!!!
My reads were sequencing at Solid and this version support this kind of read with the bowtie 1 ( I used Bowtie 1.1.1). I indexed the Phaseolus' genome (.ebtw).
$ tophat --color --quals -r -p fr-secondstrand ebwt_base_index.fa -o NGR1_NGR2_1_thout genome NFN_run6_Transcriptoma_29102013_bcSample1_F3_NGR1.csfasta NFN_run6_Transcriptoma_29102013_bcSample1_F3_NGR2.csfasta NFN_run6_Transcriptoma_29102013_bcSample1_F3_QV_NGR1.qual NFN_run6_Transcriptoma_29102013_bcSample1_F3_QV_NGR2.qual
Traceback (most recent call last):
File "/usr/bin/tophat", line 4107, in <module>
sys.exit(main())
File "/usr/bin/tophat", line 3858, in main
args = params.parse_options(argv)
File "/usr/bin/tophat", line 1008, in parse_options
self.read_params.parse_options(opts)
File "/usr/bin/tophat", line 467, in parse_options
self.mate_inner_dist = int(value)
ValueError: invalid literal for int() with base 10: '-p'
Anyone could help me to solved this?????
My reads were sequencing at Solid and this version support this kind of read with the bowtie 1 ( I used Bowtie 1.1.1). I indexed the Phaseolus' genome (.ebtw).
$ tophat --color --quals -r -p fr-secondstrand ebwt_base_index.fa -o NGR1_NGR2_1_thout genome NFN_run6_Transcriptoma_29102013_bcSample1_F3_NGR1.csfasta NFN_run6_Transcriptoma_29102013_bcSample1_F3_NGR2.csfasta NFN_run6_Transcriptoma_29102013_bcSample1_F3_QV_NGR1.qual NFN_run6_Transcriptoma_29102013_bcSample1_F3_QV_NGR2.qual
Traceback (most recent call last):
File "/usr/bin/tophat", line 4107, in <module>
sys.exit(main())
File "/usr/bin/tophat", line 3858, in main
args = params.parse_options(argv)
File "/usr/bin/tophat", line 1008, in parse_options
self.read_params.parse_options(opts)
File "/usr/bin/tophat", line 467, in parse_options
self.mate_inner_dist = int(value)
ValueError: invalid literal for int() with base 10: '-p'
Anyone could help me to solved this?????
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