Question: Is it possible to map prior to Pregap4 and Gap4?
0
gravatar for nchuang
2.1 years ago by
nchuang200
United States
nchuang200 wrote:

I sanger sequenced many reads with primers that I know the correct order. I mapped the reads to the reference sequence using bowtie. I found that Pregap4 and Gap4 have excellent manipulation and visualization of sequences and chromatograms. The only annoying thing is I have to denovo assemble each time as oppose to telling it the correct order/mapping. This sometimes leads to incorrect assemblies that I have to manually fix before polishing the sequences.

For the most part it does seem that if I use low confidence threshold it can assemble better, but then I am left with more low confidence bases to correct in the end. My other thought was I could let it do low confidence assembly but is there an option to do post assembly filtering?

pregap4 gap4 staden • 530 views
ADD COMMENTlink written 2.1 years ago by nchuang200
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: 718 users visited in the last hour