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Merge CNVnator and Lumpy to find out copy number variants

svs cnvs written 6 weeks ago by Mbillah • 100

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118

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

genome svs written 11 weeks ago by bioming • 0 • updated 11 weeks ago by WouterDeCoster ♦ 36k

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137

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News: Registration deadline: Comparative genomics

news svs snp written 4 months ago by carlopecoraro2 • 790

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1.2k

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7 follow

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Detecting Structural variants in sequencing data

structural variants calling svs sequencing written 19 months ago by Glen • 20 • updated 14 months ago by Biostar ♦♦ 20

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429

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

ngs svs pindel written 19 months ago by mehmetgoktay1989 • 0

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1.8k

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

genome bam bamsurgeon svs written 3.3 years ago by sichan • 70 • updated 23 months ago by lzy • 20

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564

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Software SVS for DNA-seq

dna-seq cattle svs rna-seq written 2.3 years ago by gabriela.ribeiro.br • 0 • updated 2.3 years ago by genomax ♦ 60k

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964

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Representative set for normal structural variation

genome structural variants svs dbvar dgv written 4.3 years ago by dmyersturnbull • 90

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Recent Replies

C: Differentially expressed genes interactome by Bastien Hervé ♦ 2.8k
Something like this : https://www.biostars.org/p/285296/ ?
C: what cause poly-G from NextSeq by genomax ♦ 60k
Any scan/trim tool should work. It would be your preference. Add bbduk.sh from BBMap suite to tha...
C: Shall I take vigna angularis or vigna radiata as a reference for vigna munga by genomax ♦ 60k
> if I take vigna radiata for annotating vigna mungo sequence You are still going to have to ...
C: what cause poly-G from NextSeq by serpalma.v • 20
what is better to remove adapters, quality and poly-G filtering: `AfterQC` or `fastp`?
C: Survival analysis with gene expression by Biologist • 130
Gud one Kevin. I have a question. On what basis Z-scale cutoff 1.0 is selected? BTW In this tut...
A: Reciprocal blast hit by colindaven • 950
I like using proteinortho for this task. It will give you a single table containing reciprocal bl...
C: Shall I take vigna angularis or vigna radiata as a reference for vigna munga by RamRS ♦ 20k
Please do not add answers unless you're answering the top-level question.
A: Shall I take vigna angularis or vigna radiata as a reference for vigna munga by rprog008 • 0
Thanks @natasha.sernova and @ genomax I found one literature, https://journals.plos.org/plosone/...
C: Overrepresented stretches of Gs in NovaSeq library by serpalma.v • 20
Thanks Michael, is there a tool that you would recomend to do the job? I am not sure if `trimmoma...
A: Single cell rna-seq (cel-seq 2) read position shift? by i.sudbery ♦ 3.2k
Sorry for the delay, but I thought I should add this for the record. CEL-Seq2 adds the UMI in th...
C: How to deduplicate UMI with mapping shift ? by i.sudbery ♦ 3.2k
You should check whether, where you see cases of reads mapping to adjacent bases with the same UM...
C: Shall I take vigna angularis or vigna radiata as a reference for vigna munga by rprog008 • 0
I think only two sequence is available Thanks I will do try to build phylogenetic tree and proc...

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