Reads from multiple movies

[jsharbrough]

Hi,

I am using Jelly2 to gap fill our genome assembly with PB reads, and I could not get Jelly2 to accept reads from multiple movies. First I tried combining subreads from multiple movies into a single bam file for blasr to map with, however blasr threw an error about mixed data sets, causing Jelly2 to fail. I then tried using an fofn containing the file names of the subread bamfiles as input for Jelly2 (which blasr v 5.3.2 allows), but Jelly2 threw an error and failed prior to sending out the mapping job to blasr.

I found a workaround where I used blasr to map the combined reads to the left and right gaps separately using an fofn as input, then started Jelly2 up at the sorting step in the Support stage. Would it be possible to allow an fofn as an acceptable input for read mapping (or, if you have already done so and I am not aware of it, advise how to make that functionality work)?

Otherwise, the Jelly2 wrapper works very nicely. I separately came up with a similar idea a few weeks ago and a friend told me about your program. I am happy that I don't have to re-invent the wheel!

Joel