How to understand the meaning of output?

[LanLBio]

Hi Prof Li,

I am curious about how to read the results file. Since there are no header and no description in the manuscript.

For example,

srf-aln.bed

Hap1Chr10	0	598	prefix#circ1-7	3.212577819676956	39397427	7	1
Hap1Chr10	645	860	prefix#circ1-7	7.834101382488479	39397427	7	1
Hap1Chr10	1335	1762	prefix#circ1-7	7.04896161086285	39397427	7	1
Hap1Chr10	1808	2129	prefix#circ1-7	8.475765485111276	39397427	7	1

srf-aln.len

prefix#circ2-510	1557996	0.9188644989499729	0.37808279015137913	0.37846257261974675
prefix#circ8-3288	388183	0.3024941409303183	0.09420134052291071	0.10453409306005174
prefix#circ4-1170	384661	0.9344680648134569	0.09334664796470571	0.09614660331296503
prefix#circ1-7	263795	4.78851708218328	0.064015793126544	0.06402380131916773

Thanks in advance, Lan

[lh3]

Need to update the document. Just briefly for now, the BED file gives: chr, start, end, SRF contig name, and mean percent identity (3.21 = 3.21%). You can ignore the rest of columns.

For the abundance estimate: SRF contig name, total length in bp, mean percent identity, filtered fraction and unfiltered fraction. If you specify -g (highly recommended!), you get the fraction of the whole genome. If you don't specify -g, you get the fraction of SatDNA.

I will keep this issue until I update README. Thanks!

[baozg]

Did the fraction have a unit or just the percentage of the whole genome? Take prefix#circ2-510 as an example, the fraction should be 0.37% or 37% if I use HiFi reads for estimation.