It’s no surprise that we have better retention of skills and knowledge that we take the time to document. I started this blog as a personal record of my academic and professional development. I keep track of articles, programming concepts, software packages, or anything else that makes me a better programmer, biologist, or scientist in general. Perhaps one day this resource may be useful to others. If nothing else, simply taking the time to frequently document things I’m learning will help me better retain the skills I have gained.



  1. dasaneesha

    Hi Daniel!

    I want to train SNAP with my transcriptome assembly file generated by the PASA software. I found your codes gff3_to_zff.pl to convert the gff3 fomat file of the spliced alignment to the zff format. It seems that the code has to be run on the spliced alignment file of the ESTs of my genome of interest against its genome. But it seems like it is not working. Is there a way that you can see my PASA-generated spliced alignment input file and tell me where I might be going wrong?

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s