interpretation of results

[Wanjie-Feng]

Hello,
thanks for developing a very useful tool, I have a little doubt when I use this tool, I would like to ask you :
My command is as follows :

perl  ./CRAQ/bin/craq -g chr.fasta -sms hifi.sorted.bam -pl T 

When I go to check the results after normal operation, I mainly focus on two files：out_final.CRE.bed and out_final.CSE.bed
The result of out_final.CRE.bed is as follows:

m01	1	1	m01:1	CRE
m01	60253887	60253887	m01:60253887	CRE
m02	1	1	m02:1	CRE
m02	44039054	44039054	m02:44039054	CRE
m02	54796608	54796608	m02:54796608	CRE
m03	1	1	m03:1	CRE
m03	11057839	11057839	m03:11057839	CRE
m03	49202667	49202667	m03:49202667	CRE
m04	1	1	Gm04:1	CRE
m04	36798166	36798166	m04:36798166	CRE
m04	55614844	55614844	m04:55614844	CRE

The result of out_final.CSE.bed is as follows:

m08	15154	15155	m08:15154	CSE
m11	27340675	27340676	m11:27340675	CSE
m17	22122332	22122333	m17:22122332	CSE
m17	24023509	24023510	m17:24023509	CSE
m17	24032958	24032959	m17:24032958	CSE

I don 't understand why the area length of my bed file is 1
Hope to get help,
thank you

[JiaoLaboratory]

HI,
Thank you very much for using CRAQ. In fact, CRAQ uses sequencing sequences to find clipping breakpoints. In the case of the “”--ser T” option, CRAQ will search the region near this breakpoint to see if there is also a cluster of low-quality base SNPs. When the length of the bed file is 1, it indicates that this position is an exact breakpoint.
As follows:

[Wanjie-Feng]

The -ser parameter is T by default, but I don 't see the corresponding information in the result. In fact, my interpretation of the result is not very clear. Can you add more information about the interpretation of the result files
Thank you

[JiaoLaboratory]

The result of out_final.CSE.bed and out_final.CRE.bed could descriped as:
chrid error_start error_end error_breakpoint error_stype
m17 22122332 22122333 m17:22122332 CSE

for your result, error_start = error_end, it is normal, means there is no mapping gap near breakpoint (above figure left ).

[JiaoLaboratory]

[Wanjie-Feng]

Thank you for your reply and explanation,
best wishes