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157

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

ngs svs pindel written 3 months ago by mehmetgoktay1989 • 0

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174

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Detecting Structural variants in sequencing data

structural variants calling svs sequencing written 3 months ago by Glen • 0

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1.2k

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

genome bam bamsurgeon svs written 2.0 years ago by sichan • 50 • updated 7 months ago by lzy • 0

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287

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Software SVS for DNA-seq

dna-seq cattle svs rna-seq written 11 months ago by gabriela.ribeiro.br • 0 • updated 11 months ago by genomax ♦ 33k

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663

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Representative set for normal structural variation

genome structural variants svs dbvar dgv written 2.9 years ago by dmyersturnbull • 70

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Recent Replies

C: Refseq Proteins For A Given Taxid by yarmda • 0
I don't know if this will still get any attention, but I am running into RuntimeError: Search Bac...
C: Where to download blacklisted regions? by abhishekniroula7 • 50
Hi @Friederike and @venu Why are hg38 and hg19 list different?
C: Converting narrowPeak to bed by Spacebio • 80
I tried but it is not working, any other suggestion? Thanks for your help!
C: Analyzing specific genes in a microarray (RNA expression) by genomax ♦ 33k
Take a look at these previous threads: https://www.biostars.org/p/74337/ and https://www.biostars...
C: Converting narrowPeak to bed by Spacebio • 80
I have the narrowPeak files, I want to extract the counts to use the matrix with DESeq or EdgeR. ...
A: Analyzing specific genes in a microarray (RNA expression) by h.mon ♦ 8.6k
> Is it correct to only take probes related with cell differentiated > genes from my txt fi...
C: Different alignment rates for Hisat2 and STAR, Hisat2 has lower alignment rate a by genomax ♦ 33k
It is better to stick with one aligner for a project. NGS aligners have many nuances built in (ke...
A: Converting narrowPeak to bed by Rory Stark • 170
`DiffBind` supports `narrowPeak` format directly, Just specify "`narrow`" as the value for `PeakC...
A: What kind of advantage does PEAR bring? by h.mon ♦ 8.6k
> 1) How PEAR treat un-overlapped PE reads? discard them? -o Specify the name to be u...
A: ATACseq with STAR and macs2 by simon.vanheeringen • 20
Have you tried the pipeline from the Kundaje lab? https://github.com/kundajelab/atac_dnase_pipe...
C: A confusion regarding haplotype by shoujun.gu • 220
Now I may understand what the post means...
A: Feature/Motif Extraction from Sequences? by simon.vanheeringen • 20
Given your clarification, I think kmer-SVM does exactly what you want. You can train and evaluate...

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