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 notifications@github.com 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

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[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 https://github.com/MariaNattestad/Assemblytics/commit/3db55120e7f45c8fbbf14bf0f26186682c465689. If you use version 1.2.1 it should work. Thank you!