search

zhixingfeng / iGDA

Detect and phase minor SNVs from long-read sequencing data
GNU General Public License v2.0
15 stars 0 forks source link

haplotype frequency #8

Open antoine4ucsd opened 2 years ago

antoine4ucsd commented 2 years ago

Hello is there an option to store frequency, Avg Coverage, num reads, for each haplotype ... that would be nice to save it in the fasta header for each. thank you and congrats for all the good work!

zhixingfeng commented 2 years ago

Hi antoine4ucsd, Frequency is not wrapped into fasta files in the current pipeline, but reads count for each contig can be found in the .count files in the intermediate results.

Or, there is an internal CLI "igda abundance" can yield reads count for each contig. You might have a try on that using the intermediate results as input.

Best

Zhixing

antoine4ucsd commented 2 years ago

thank you . reads.count is already a good metric to get. Frequencies and counts in contig names would be something nice to add in the future.

antoine4ucsd commented 2 years ago

Hello I am analyzing a new set of NP data. I have interesting results but I would like to have the abundance (and ideally the mean coverage) for each haplotype. is it something I can get from igda? all suggestions are welcome

thank you@

PeienJ commented 1 year ago

Hello Zhixing, Could you please give an example of how to use "igda abundance" or .count files? There are many intermediate files and I started to be confused about which file I should use. Thanks!!