Question: Estimate insert size for pacbio long reads
0
gravatar for arunprasanna83
8 weeks ago by
arunprasanna8330 wrote:

I am trying to use pacbio long reads to do gap filling using GapFiller program. What is the correct way of specifying the insert size mentioned in library file ? In other words, how to estimate insert size for pacbio long reads (SMRT).

Thanks in Advance.

gapfilling next-gen assembly • 158 views
ADD COMMENTlink written 8 weeks ago by arunprasanna8330

You should probably use PBJelly (https://sourceforge.net/p/pb-jelly/wiki/Home/). Here are some instructions for running PBJelly for PacBio Sequel subreads and error correcting using a variant caller instead of Pilon to correct indels (. I also have another gist if you want to some instructions to run Pilon (, but I have found that BBTool's variant caller CallVariants.sh) did a better job in terms of BUSCO scores and RNA-Seq mapping rates than running Pilon.

ADD REPLYlink written 8 weeks ago by jean.elbers530
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2486 users visited in the last hour