How to calculate the mapping rate?

[CaiCheng1996]

After GEM2, how to directly get the mapping rate ? or I should calculate by myself? than how? Btw, if I directly use "samtools flagstat" on the BAM files from "bed2D_to_BAMhic", the mapping rate is 100%, which is impossible.

[david-castillo]

Hi,

To get the percentage of mapped against input reads have a look at the plots of fragment or iterative based mapping in the tutorial http://3dgenomes.github.io/TADbit/tutorial/tutorial_5-Parsing_mapped_reads.html

We use a pseudoBAM file where the flags are used to store the read filter category and not the usual SAM data (read paired, first in pair, etc. ). Moreover, the BAM file is mirrored (there are two entries per interaction) to easily access paired data. Better use the tsv files that you created before the BAM file.

Regards

David

[CaiCheng1996]

Hi, Thank you for the reply. I already followed the tutorial http://3dgenomes.github.io/TADbit/tutorial/tutorial_5-Parsing_mapped_reads.html and got those plots, but I really didn’t see any precise numbers representing “percentage of mapped reads” in those plots, this may be due to my lack of knowledge and experience.  I know the information in those plots are important, but I just want to get an accurate number representing my mapping rate, so could you please tell me in more detail, which step or which plot can help me get the number?

Thanks!