Question: Problem Assembling Breakdancer Output With Tigra
1
gravatar for roalva1
6.3 years ago by
roalva180
Spain
roalva180 wrote:

Hello,

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,

Regards

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ADD COMMENTlink modified 5.7 years ago by Biostar ♦♦ 20 • written 6.3 years ago by roalva180
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