User: trausch
trausch • 730
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Posts by trausch
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Comment:
C: ATACseq with STAR and macs2
... We use Bowtie for mapping, MACS for peak calling, IDR filtering of peaks and DESeq2 for differential peaks. Still work in progress but our current pipeline is on [github][1].
[1]: https://github.com/tobiasrausch/ATACseq ...
written 3 days ago by
trausch • 730
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... It is a tab-delimited text file. You can use datamash to convert it to row-format:
cat outprefix.metrics.tsv | datamash transpose | column -t
The column-format is useful if you want to compare statistics across multiple samples because you can just concatenate the metrics files.
...
written 8 days ago by
trausch • 730
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... You can try [alfred][1] (disclaimer: our own tool). Example plots are here:
[WGS][2] and [WES][3]. It also supports feature counting for RNA-Seq.
[1]: https://github.com/tobiasrausch/alfred
[2]: https://raw.githubusercontent.com/tobiasrausch/alfred/master/exampleplots/NA06985.pe.pdf
[3]: ht ...
written 10 days ago by
trausch • 730
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... There is an online [Cancer Genomics Tutorial][1] available for Delly that explains many of these INFO fields. There is also a separate [Delly user group][2] that has some info about this.
[1]: https://www.gitbook.com/book/tobiasrausch/tutorial-delly/details
[2]: https://groups.google.com/forum ...
written 17 days ago by
trausch • 730
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... We recently set up the web application [Indigo][1] that can analyze Sanger traces and aligns them to a reference genome or wildtype chromatogram. The [standalone command-line version][2] has a couple more features like dumping the whole Sanger trace as a tab delimited file so you can then indeed edi ...
written 17 days ago by
trausch • 730
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Answer:
A: Structural Variant annotation
... SVs are usually reported in VCF format. Such a VCF you can then annotate with [SnpEff][1], [VEP][2] or [Annovar][3]. Conversion to MAF for a tumor-normal VCF should be possible with [vcf2maf][4].
[1]: http://snpeff.sourceforge.net/
[2]: http://www.ensembl.org/info/docs/tools/vep/index.html
[ ...
written 17 days ago by
trausch • 730
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... Thanks, I have not created a Tools page in Biostars but there is a fairly extensive [README][1] on github.
[1]: https://github.com/tobiasrausch/alfred ...
written 23 days ago by
trausch • 730
3
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... Looks like a processed pseudogene of SLC6A8 in that patient (gene retrocopy insertion polymorphism). ...
written 25 days ago by
trausch • 730
0
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467
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... Yes, there are statically compiled binaries available [here][1] and we did run it previously on Nanopore, Illumina and PacBio reads but if you experience any problems please let me know.
[1]: https://github.com/tobiasrausch/alfred/releases ...
written 26 days ago by
trausch • 730
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... Maybe there is a more elegant solution but pipes should work:
zcat custom1.vcf.gz | bcftools annotate -a custom2.vcf.gz -c INFO/CustomTwo - | bcftools annotate -a custom3.vcf.gz -c INFO/CustomThree - ...
written 4 weeks ago by
trausch • 730
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10 days ago,
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For A: list of gene or transcript IDs and their length
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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11 weeks ago,
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: Methods of classifying, not detecting, structural variation?
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20 months ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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20 months ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: Methods of classifying, not detecting, structural variation?
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For A: Methods of classifying, not detecting, structural variation?
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For A: Methods of classifying, not detecting, structural variation?
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