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Detecting Structural variants in sequencing data

structural variants calling svs sequencing written 10 months ago by Glen • 0 • updated 5 months ago by Biostar ♦♦ 20

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288

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Running Pindel individually per sample rather than running everything as it expects

ngs svs pindel written 10 months ago by mehmetgoktay1989 • 0

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1.5k

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Anyone used BAMSurgeon to spike in 1KB insertions/deletions?

genome bam bamsurgeon svs written 2.6 years ago by sichan • 60 • updated 14 months ago by lzy • 0

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421

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Software SVS for DNA-seq

dna-seq cattle svs rna-seq written 18 months ago by gabriela.ribeiro.br • 0 • updated 18 months ago by genomax ♦ 46k

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827

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Representative set for normal structural variation

genome structural variants svs dbvar dgv written 3.5 years ago by dmyersturnbull • 70

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Recent Replies

A: Plotting multiple signal files against a single genomic region by Alex Reynolds ♦ 23k
Make a [custom track][1] in the UCSC Genome Browser, setting bigWig-sourced signal tracks in "pac...
C: Illumina exome beadchip duplicated positions by miaowzai • 30
This makes a lot of sense! Thank you so much.
C: Human genes correlation to Bacterial genes by saamar.rajput • 10
To identify bacterial and human genes with similar expression kinetics
C: find overlapping sequences and report min start and max end positions by Nicolas Rosewick • 6.2k
As you tagged the question with the R tag I guessed it should be in R. But using bedools is also ...
C: Hybrid assembly using MinION data + correction with Illumina. Which strategy to by Damian Kao ♦ 14k
Try all of them. In my experience there isn't one method that just works all the time. Sometimes ...
A: How do you organize sequence data (FASTQs)? by Pierre Lindenbaum ♦ 106k
> How do you retrain metadata regarding the sequencing data? don't store fastq, use ubam and ...
C: How do you organize sequence data (FASTQs)? by Pierre Lindenbaum ♦ 106k
see also this old post https://www.biostars.org/p/821/ (8 years ago ?!)
A: infer top level go category from GO:ID by Vijay Lakhujani • 1.9k
Hi [Carambakaracho][1] API's to the rescue! ;) I suppose this project being part of a large sof...
C: How to calculate distribution of mapped read over classes of RNA? by biplab • 40
That's true. Is there any option in bedtools to count only uniquely mapped reads? I did not find ...
A: How do you organize sequence data (FASTQs)? by Vijay Lakhujani • 1.9k
> How do you organize your sequencing data? Renaming the files works best for me. For e.g. ...
C: using awk to extract a specific pattern by Damian Kao ♦ 14k
Have you tried the -y parameter in gffread: -y write a protein fasta file with the transl...
C: How do you organize sequence data (FASTQs)? by genomax ♦ 46k
> How do you backup your sequence data? Use NCBI SRA as your backup (in addition to other thi...

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