I have one output file from breakdancer, then, as I have multiples breakpoints for the same sv, I want to do a local assembly with tigra. Once I' ve done with this command:
/clinicfs/naranjoma/software/tigra-sv/build/bin/tigra-sv -R citrus_clementina.fasta -b sv.txt ivia_095_realigned_fixed.bam I get 8 files for each sv like these: scaffold_2.7102763.scaffold_3.4752728.CTX.449.--.1351.7102063.4752028.fa.contigs.fa scaffold_2.7102763.scaffold_3.4752728.CTX.449.-+.1351.7102063.4752028.fa.contigs.fa scaffold_2.7102763.scaffold_3.4752728.CTX.449.+-.1351.7102063.4752028.fa.contigs.fa scaffold_2.7102763.scaffold_3.4752728.CTX.449.++.1351.7102063.4752028.fa.contigs.fa scaffold_2.7102763.scaffold_3.4752728.CTX.449.--.1351.7102063.4752028.fa.contigs.het.fa scaffold_2.7102763.scaffold_3.4752728.CTX.449.-+.1351.7102063.4752028.fa.contigs.het.fa scaffold_2.7102763.scaffold_3.4752728.CTX.449.+-.1351.7102063.4752028.fa.contigs.het.fa scaffold_2.7102763.scaffold_3.4752728.CTX.449.++.1351.7102063.4752028.fa.contigs.het.fa
So I have some questions: 1. which is the difference among these files? They seem that are related to the same sv, but I don't get the difference, even though the content is different. 2. Are these sv already the good sv? Do I have to filter out anything? 3. Inside of the files the header looks like this: ">Contig1 366 34.95 20 I-8:4,-3:25, O 1 3", what do the numbers mean? 4. If I have several samples, how can I distinguish among them?
Thanks a lot,