I am looking for a way to obtain a bed file that contains the coordinates for all of the filled gaps in the PBJelly output fasta. I see that such a file is made for all the gaps in the initial assembly, but I cannot seem to find something similar for the output assembly.
I would like to visualize areas of the genome that used to be gaps, but have since been either filled or partially filled by PBJelly.
Thank you
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There isn't a user-friendly file provided currently. However, all of the PBJelly gap-filling sequence is lower-cased in the output reference which could be used to identify gaps.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I am looking for a way to obtain a bed file that contains the coordinates for all of the filled gaps in the PBJelly output fasta. I see that such a file is made for all the gaps in the initial assembly, but I cannot seem to find something similar for the output assembly.
I would like to visualize areas of the genome that used to be gaps, but have since been either filled or partially filled by PBJelly.
Thank you
There isn't a user-friendly file provided currently. However, all of the PBJelly gap-filling sequence is lower-cased in the output reference which could be used to identify gaps.
Thank you for the response Adam English. Identifying the lower case sequences should be sufficient.