tophat2 -o/--output-dir unavailable

[wskwxf]

You should not use options after your input. Otherwise tophat will not recoganize those arguments and use its default ( in your case it created its default directory tophat_out)

Usage: tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]

You command should look like this:

nohup tophat2 -o Htest_out /share/nas2/heh/data/genome/hs_ref_GRCh37.p5_chr_all.format.fa Htest_1.fq Htest_2.fq &

You are right.Thanks!

[santhilalsubhash]

You should not use options after your input. Otherwise tophat will not recoganize those arguments and use its default ( in your case it created its default directory tophat_out)

Usage: tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]

You command should look like this:

nohup tophat2 -o Htest_out /share/nas2/heh/data/genome/hs_ref_GRCh37.p5_chr_all.format.fa Htest_1.fq Htest_2.fq &

[wskwxf]

Could you please post your command you used for running?

my command:
nohup tophat2 /share/nas2/heh/data/genome/hs_ref_GRCh37.p5_chr_all.format.fa Htest_1.fq Htest_2.fq -o Htest_out &
it created output directory is tophat_out,not Htest_out.

[santhilalsubhash]

Could you please post your command you used for running?

[Wallysb01]

Check you paths and if you have the needed permissions to make that directory. You could have one of the parts of the path wrong or you can’t create a new directory in the directory that tophat_out is going. I don’t think this is a bug, I just used this myself a few days ago (on the newest version).

[wskwxf]

I use tophat-2.0.10 ,but the -o/--output-dir option is unavailable? That is bug or myself use problem?