Question about output
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 citrusclementina.fasta -b sv.txt ivia095realignedfixed.bam I get 8 files for each sv like these: scaffold2.7102763.scaffold3.4752728.CTX.449.--.1351.7102063.4752028.fa.contigs.fa scaffold2.7102763.scaffold3.4752728.CTX.449.-+.1351.7102063.4752028.fa.contigs.fa scaffold2.7102763.scaffold3.4752728.CTX.449.+-.1351.7102063.4752028.fa.contigs.fa scaffold2.7102763.scaffold3.4752728.CTX.449.++.1351.7102063.4752028.fa.contigs.fa scaffold2.7102763.scaffold3.4752728.CTX.449.--.1351.7102063.4752028.fa.contigs.het.fa scaffold2.7102763.scaffold3.4752728.CTX.449.-+.1351.7102063.4752028.fa.contigs.het.fa scaffold2.7102763.scaffold3.4752728.CTX.449.+-.1351.7102063.4752028.fa.contigs.het.fa scaffold2.7102763.scaffold3.4752728.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
-
Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
Long-read sequencing has seen remarkable advancements,...12-02-2024, 01:49 PM -
The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben MartÃnez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...11-06-2024, 07:24 PM