Question: check if one unitig is truly circual
0
gravatar for orange
5.6 years ago by
orange30
Korea, Republic Of
orange30 wrote:

For bacteria assembly with pacbio reads, a unitig is easy at most time. But how to check if it is truly circual ?

I tried CA_best_edge_to_GML.py,and an error happen like "

Traceback (most recent call last):
File "CA_best_edge_to_GML.py", line 51, in 
id1, lib_id, best5, o1, best3, o3 = l
ValueError: too many values to unpack

So I changed line 51 to id1, lib_id, best5, o1, best3, o3 = l[:6] ,and line 51 works ,but another error happens:

Traceback (most recent call last):
File "CA_best_edge_to_GML.py", line 52, in 
G.add_node(id1, unitig="utg%s" % frg_to_tig[id1])
KeyError: '8' 

so how to solve it ? Or any other way to check if contig is truly circual ?

Thanks!

celera • 1.2k views
ADD COMMENTlink modified 5.6 years ago by rhall160 • written 5.6 years ago by orange30
2
gravatar for rhall
5.6 years ago by
rhall160
United States
rhall160 wrote:

For an up to date Celera to Gephi script:

https://github.com/PacificBiosciences/Bioinformatics-Training/blob/master/scripts/CeleraToGephi.py

General circularization and trimming:

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Circularizing-and-trimming

Video how to:

http://files.pacb.com/Training/CircularContigConfirmationGepard/story.html

ADD COMMENTlink written 5.6 years ago by rhall160
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