Dear Maria,
When I used the command-line Assemblytics software to do the SV calling, there are some errors in the *. Assemblytics_structural_variants.bed file.
My script to run Assemblytics is Assemblytics-master/scripts/Assemblytics Sample1.contig.fa.delta Sample1 10000 20 100000
For example: there is no #reference output in the column 1 of some lines (line2). I have already tried several samples, some samples with this problem, but some samples without it.
I will be very grateful if you can help me.
Many thanks!
reference ref_start ref_stop ID size strand type ref_gap_size query_gap_size query_coordinates method
Dear Maria, When I used the command-line Assemblytics software to do the SV calling, there are some errors in the *. Assemblytics_structural_variants.bed file. My script to run Assemblytics is Assemblytics-master/scripts/Assemblytics Sample1.contig.fa.delta Sample1 10000 20 100000 For example: there is no #reference output in the column 1 of some lines (line2). I have already tried several samples, some samples with this problem, but some samples without it. I will be very grateful if you can help me. Many thanks!
reference ref_start ref_stop ID size strand type ref_gap_size query_gap_size query_coordinates method
Chr11 2464132 2464153 Assemblytics_w_2 21 + Deletion 21 0 Contig3:15142667-15142667:+ within_alignment Chr11 2794455 2794480 Assemblytics_w_3 25 + Deletion 25 0 Contig3:14807841-14807841:+ within_alignment Chr11 2796811 2796837 Assemblytics_w_4 26 + Deletion 26 0 Contig3:14810184-14810184:+ within_alignment