felixgrewe/map_n_extract

test pipe

Opened this issue · 4 comments

felixgrewe commented

Would you please test if the installation is working? You'd need to install all required programs and many Perl modules.

I created test files in the test_files_for_local_use folder. The links to NGS reads in the table are pointing to files on vortex. If you want to test install on your computer you'd need to download the reads.

I added the Sticta CEGMA output to the test_files_for_local_use folder. You can test run the script using one as the reference and map the reads of the other and vice versa.

Erythroxylum commented

I just realized I do not have any way of downloading the reads to the computer here at UIC if they are on Vortex. Felix, will you be in your office tomorrow? I will come to FM to run the program.

felixgrewe commented

for the test of the script no trimming is necessary

Erythroxylum commented

Is there a way to access Vortex remotely? If not, I cannot get the reads here. Felix, will you be in your office tomorrow? I will come in to FM and finish running the program.

felixgrewe commented

@Erythroxylum @twidhelm @robertonion51
Please do not directly change the repo. Use a branch or fork and pull request instead.