search

Shamir-Lab / Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
58 stars 7 forks source link

recycler output #1

Closed cytang19 closed 8 years ago

cytang19 commented 8 years ago

Hi,

I am trying to use your program. There is no description on the output so I am not sure if I am doing correctly. My output is a text file with all the EDGEs, for ex: ('EDGE_132_length_60_cov_85', 'EDGE_623_length_203_cov_23.7027').

Is this suppose to be the output? Do you have a way where I can extract the sequence from the fastg file?

Thanks, Cheng

rozovr commented 8 years ago

Hi Cheng,

thanks for the feedback. I updated the README on the front page here to describe the outputs. I suspect what you are seeing is file .cycs.paths_w_cov.txt. The sequences are in a separate file that should be labeled .cycs.fasta.

Best, Roye

cytang19 commented 8 years ago

Hi Roye,

I didn't realise there are 2 output files until now that you told me. All the time I was seeing only the screen output. Thanks for your help.

Cheers, Cheng