Problem with running tophat

[luana]

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?????

[mastal]

If you use the parameter -r, then you need to specify an integer value for -r, the mate inner distance (distance between the two reads of a pair).

Otherwise, if you don't specify -r, the tophat manual says the default value is 50.

[luana]

Now I don't specify the -r and this message appeared..the files indexes are at directory

tophat --color --quals fr-secondstran genome.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

[2016-06-17 15:24:41] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2016-06-17 15:24:41] Checking for Bowtie
Bowtie version: 1.1.1.0
[2016-06-17 15:24:41] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie index files (fr-secondstran.*.ebwt)

What's the problem?

[GenoMax]

You have not specified the "basename" (ebwt_base_index, if that is the name) of the index files for the genome that you are searching against.

[mastal]

Hi Luana,

You are missing the final 'd' from fr-secondstrand, and you are also
missing the /path/to/ the bowtie index (give only the prefix of the index name).

[luana]

Hi Guys,
I'm trying to fix this script but the problem persist. I put the "d" in the fr-secondstrand, but I didn't understand witch file from index directory I have to use.
When I indexed the genome I used the fasta file and I had six files .ebwt
How file index .ebwt I have to use in this script?

tophat --color --quals fr-secondstrand /bowtie/bowtie-index/ebwt_base -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

[2016-06-22 10:12:38] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2016-06-22 10:12:38] Checking for Bowtie
Bowtie version: 1.1.1.0
[2016-06-22 10:12:38] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie index files (fr-secondstrand.*.ebwt)

[mastal]

you use what is know as the 'prefix', the common part of the filename before the .ebwt, so all 6 of your index files should have the same 'prefix'.

Also, do you have single-end or paired-end reads? If your reads are single-end, then you should have a comma instead of a space between the names of the two read files, and between the names of the 2 quality files.