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Merge CNVnator and Lumpy to find out copy number variants

svs cnvs written 6 months ago by Mbillah • 110 • updated 7 weeks ago by Mant • 0

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182

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Germline and somatic model, which one is preferred to call SVs fish male and female population

genome svs written 7 months ago by bioming • 0 • updated 7 months ago by WouterDeCoster ♦ 39k

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216

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News: Registration deadline: Comparative genomics

news svs snp written 10 months ago by carlopecoraro2 • 920

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7 follow

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Detecting Structural variants in sequencing data

structural variants calling svs sequencing written 2.0 years ago by Glen • 20 • updated 20 months ago by Biostar ♦♦ 20

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511

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

ngs svs pindel written 2.0 years ago by mehmetgoktay1989 • 0

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2.0k

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

genome bam bamsurgeon svs written 3.8 years ago by sichan • 70 • updated 2.3 years ago by lzy • 20

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611

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Software SVS for DNA-seq

dna-seq cattle svs rna-seq written 2.7 years ago by gabriela.ribeiro.br • 0 • updated 2.7 years ago by genomax ♦ 68k

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1.0k

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Representative set for normal structural variation

genome structural variants svs dbvar dgv written 4.7 years ago by dmyersturnbull • 90

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Recent Replies

A: Reads per COG normalization by Mensur Dlakic • 40
> Is there some way to normalize the number of reads mapped to each COG taken this information...
A: Megahit Assembly - command line error by Mensur Dlakic • 40
This part of your command **./megahit** means that you have a *megahit* executable in the present...
C: Reads per COG normalization by Asaf ♦ 5.9k
There are a lot of ways to normalize the data, the only question is why do you want to normalize it?
C: Megahit Assembly - command line error by Asaf ♦ 5.9k
Do you get an error?
C: limma voom - mean variance trend by furrdinand • 0
Yes, I used calcNormFactors with the TMM method prior to voom normalization on the dge object.
C: ABySS OpenMP version by SMK • 1.4k
No worries, updated by [https://www.biostars.org/u/23882/][1] already. [1]: https://www.biost...
A: How to find out human mtDNA genes in d-loop control region for Indian origin onl by grant.hovhannisyan • 1.6k
D-loop is a non-coding region, so it does not contain genes. Most probably you are looking for m...
C: Distinguishing between different formats for VCF file indexes by cmdcolin • 1.2k
Probably you can tell by the file extension. IDX is a "tribble index" and TBI is a tabix index
C: ABySS OpenMP version by SMK • 1.4k
You might need to edit the post (not to use the code chunk mode) to increase the readability.
A: Filtered a .vcf file based on id of a second file by cerriguglielmo • 0
Ok, the sample file contains the id while the file contains all data: The command that generate t...
C: How to do data cleaning for VCF genetic file by Shicheng Guo • 7.5k
the remaining task includes: Statistics: Alternative allele frequency > 0.5 sites: 3...
C: Unable to find FASTA index entry for 'unitig_2993_pilon error. by tmrhyd • 0
Nothing happened for either? the command didn't run a error, but didn't return any input either.

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