scaff_screeN not found about scaff10x

[andreaswallberg]

I have the same issue. @hyperoplus did you solve it?

[andreaswallberg]

Dang! The solution is of course in the documentation:

The binary needs to be called using the full path:

/full/path/to/Scaff10X/src/scaff10X

Then it works for me :-)

[hyperoplus]

Hi Andreas, many thanks for pointing this out, didn't notice this in the documentation.

It seems to be running ok now!

[andreaswallberg]

@hyperoplus

Glad I could help! Actually, can I ask for a favor as we both seem to be pushing our way through the tool chain for the first time?

I got stuck further into the process as I suspect that Scaff10x does not like the way my chromium barcodes are encoded in the BAM files (as "BX:Z:" tags) that I provide.

Can you please send a few lines of SAM read mappings that the program accepts (or generates itself if you give it fastq files) in your case, so that I can check what kind of reformatting I need to accomplish?

You can find my email under my profile. Cheers!