Closed dcopetti closed 6 years ago
Hi Dario,
To use tigmint, your command should look something like this:
tigmint-make tigmint draft=myassembly reads=myreads
In this example, tigmint would expect to find a draft assembly myassembly.fa and chromium reads (post-longranger) myreads.fq.gz in your current working directory.
For your case, I would make a soft link to your barcoded.fq.gz reads file in your 'tigmint' directory, and run the command:
tigmint-make tigmint draft=Rabiosa_genome reads=barcoded
That should produce a molecule TSV file like you mentioned above, and a number of other output files.
Let me know if that helps! Lauren
Hi Lauren, Thanks for the suggestion, with the symlink it works now (in the message above I also did not paste the whole command I was running). Dario
Great - I'm glad you got it working!
Hi, After running successfully longranger
longranger basic --id=4606 --fastqs=input_fastqs --localcores=4 --localmem=30
I am running tigmint-span but I am getting this error:I had to rename the .fastq.gz to fq.gz file, and the rest seems fine to me:
I am wondering if I should have that .tsv file created at some point. Or what is the reason for this issue? Thanks, Dario