Hi,
I am quite new to Bioinformatics. I wanted to ask if anyone has any idea as I am kind of stuck.
I am using Badreads for simulating Oxford Nanopore long reads and then used BWA for mapping the short reads to these simulated long reads where these set of long reads acts as my reference in BWA.
The short reads are generated from a graph where the short reads are basically the edges. The nodes also contain some characters. for example: if a node's characters are AACG and the suffix attached to it is GTA the the prefix of the following node is AA and the node is CGGTA.
So the suffix of one node along with that node's characters is equal to the next node's prefix and that node's characters.
After that I have written a program where the output is the set of files and each file is named as LR1 for Long read 1 and it consists of all the short reads (both for prefix and suffix) this long read has mapped to.
I have also done where it just checks contiguity for like one step. Like I checked for one particular long read how many instances are there where the node's characters + suffix's character = prefix's character + node's character as then they are actually contiguous in the original graph.
Now I want to find how much contiguously (maximum) this LR1 is mapping. Can anyone share any ideas?
Thanks a lot.
