Output bed file has no chromosomes in the first column

[lxxiaoxiaLi]

Hi Maria,
thanks for this wonderful tool. I find the output bed file I generate (I'm running Assemblytics） has no chromosomes in the first column , but When I let my sample.delta files upload to the website(http://assemblytics.com/), the output bed file has chromosomes in the first column, So I want to why? How should I solve this problem?
#reference ref_start ref_stop ID size strand type ref_gap_size query_gap_size query_coordinates method
3011968 3012034 Assemblytics_w_1 66 + Deletion 66 0 :139517-139517:+ within_alignment
3183128 3183182 Assemblytics_w_2 54 + Deletion 54 0 :310092-310092:+ within_alignment
3209069 3209153 Assemblytics_w_3 84 + Deletion 84 0 :335922-335922:+ within_alignment
3644058 3644058 Assemblytics_w_5 55 + Insertion 0 55 :750072-750127:+ within_alignment
3837286 3837286 Assemblytics_w_6 78 + Insertion 0 78 :942419-942497:+ within_alignment
4264770 4264825 Assemblytics_w_7 55 + Deletion 55 0 :1368592-1368592:+ within_alignment
4673304 4673387 Assemblytics_w_8 83 + Deletion 83 0 :1728231-1728231:+ within_alignment
4968463 4968463 Assemblytics_w_9 69 + Insertion 0 69 :1940538-1940607:+ within_alignment
5364412 5364472 Assemblytics_w_10 60 + Deletion 60 0 :2334363-2334363:+ within_alignment
5546544 5546544 Assemblytics_w_11 78 + Insertion 0 78 :2500330-2500408:+ within_alignment

Best Regards,
Xiaoxia Li

[MariaNattestad]

Can you share the first several lines of your delta file? The chromosome/contig names come from the headers in the delta file.

…

On Wed, Jul 15, 2020 at 12:14 AM lxxiaoxiaLi ***@***.***> wrote: Hi Maria, thanks for this wonderful tool. I find the output bed file I generate (I'm running Assemblytics has no chromosomes in the first column , but When I let my sample.delta files upload to the website(http://assemblytics.com/), the output bed file has chromosomes in the first column, So I want to why? How should I solve this problem? #reference ref_start ref_stop ID size strand type ref_gap_size query_gap_size query_coordinates method 3011968 3012034 Assemblytics_w_1 66 + Deletion 66 0 :139517-139517:+ within_alignment 3183128 3183182 Assemblytics_w_2 54 + Deletion 54 0 :310092-310092:+ within_alignment 3209069 3209153 Assemblytics_w_3 84 + Deletion 84 0 :335922-335922:+ within_alignment 3644058 3644058 Assemblytics_w_5 55 + Insertion 0 55 :750072-750127:+ within_alignment 3837286 3837286 Assemblytics_w_6 78 + Insertion 0 78 :942419-942497:+ within_alignment 4264770 4264825 Assemblytics_w_7 55 + Deletion 55 0 :1368592-1368592:+ within_alignment 4673304 4673387 Assemblytics_w_8 83 + Deletion 83 0 :1728231-1728231:+ within_alignment 4968463 4968463 Assemblytics_w_9 69 + Insertion 0 69 :1940538-1940607:+ within_alignment 5364412 5364472 Assemblytics_w_10 60 + Deletion 60 0 :2334363-2334363:+ within_alignment 5546544 5546544 Assemblytics_w_11 78 + Insertion 0 78 :2500330-2500408:+ within_alignment Best Regards, Xiaoxia Li — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#35>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4W4PKQEOMUOZQNC2SI7ADR3VJOXANCNFSM4O2HWEGQ> .

[lxxiaoxiaLi]

delta file as below:
NH002.fa NH001.fa
NUCMER

Chr9 ctg1 23012720 17943667
2873122 2981468 1893 109489 1307 1307 0
18
1
14
25
1
1
6
1
13
2
9
1
-37
-1
-1
-1
-1
-1
-1
-1
-1
-2
175
135
1
1
1
1
2
1
1
5
2
68
10
4
5
1
1
4
8
4
10
4
30
7
4
-145
-1
-1
-1
-1
-1
-1
-1
-1
-2
146
1
1
4
1
1
1
1
1
90
12
3
9
1
1
-9
23
1
1
1
1
5
1
1
1
3
15
1
1
12
5
1
6
19
9
12
-9
41
1
1
194
1
5
4
5
8
6
14
5
2
19
11
16
6
11
1
150
12
1
6
1
30
1
1
3
2
1
5
2
5
15
19
1
5
21

[MariaNattestad]

Thanks for bringing this to my attention! I was able to reproduce the error and fix it. See 3db5512. If you use version 1.2.1 it should work.
Thank you!