minimap to make a comparison between reference to de novo assembly

Question

[Lissa Cruz Saavedra]

Hi

I am trying to compare between my reference fasta file versus some de novo assembly (that includes just a sequences from family of proteins in fasta format after run blast).

I am using the following commands:

minimap2 -cx asm5 --cs /shared2/salmosim/lissa/fasta/TriTrypDB-41_TcruziSylvioX10-1_Genome.fasta CG_1.fasta

when I try to get a stats, I have that results

Number of mapped sequences: 990
Number of primary alignments: 7773
Number of secondary alignments: 7527
Number of primary alignments with >65535 CIGAR operations: 0
Number of bases in mapped sequences: 357654
Number of mapped bases: 489493
Number of insertions in [0,50): 12706
Number of insertions in [50,100): 10
Number of insertions in [100,300): 0
Number of insertions in [300,400): 0
Number of insertions in [400,1000): 0
Number of insertions in [1000,inf): 0
Number of deletions in [0,50): 661
Number of deletions in [50,100): 7
Number of deletions in [100,300): 0
Number of deletions in [300,400): 0
Number of deletions in [400,1000): 0
Number of deletions in [1000,inf): 0

Bur if try to call the SV everyone is 0.

minimap2 -cx asm5 --cs /shared2/salmosim/lissa/fasta/TriTrypDB-41_TcruziSylvioX10-1_Genome.fasta CG_1.fasta CG_1.fasta | sort -k6,6 -k8,8n | paftools.js call -L20000 - > var.txt

I am a beggining in this software, so actually i don't have idea what is happening.

All you help could be a lot of useful to me.

Thank you so much.

[ATpoint]

Hi Lissa Cruz Saavedra, I added some markdown to your post to highlight code and data examples using the code option (10101) from the format bar. Also, please avoid capslock in the title as this is generally considered impolite because it implies shouting.

[Lissa Cruz Saavedra]

Thank you so so much!. I didn't know, your so kind!