User: trausch

gravatar for trausch
trausch730
Reputation:
730
Status:
Trusted
Location:
Germany
Website:
http://tobiasrausch.gi...
Scholar ID:
Google Scholar Page
Last seen:
15 hours ago
Joined:
2 years, 3 months ago
Email:
r*********@gmail.com

Posts by trausch

<prev • 78 results • page 1 of 8 • next >
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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 trausch730
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... 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 trausch730
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Answer: A: Calculating coverage for WGS, WES and RNASeq
... 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 trausch730
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Answer: A: Explain the definition of DELLY output
... 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 trausch730
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Answer: A: Any suggestion for sanger sequencing result editing
... 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 trausch730
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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 trausch730
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... 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 trausch730
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Answer: A: Soft and Hard Clipping issue - abnormal IGV profile
... Looks like a processed pseudogene of SLC6A8 in that patient (gene retrocopy insertion polymorphism). ...
written 25 days ago by trausch730
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... 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 trausch730
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Comment: C: Merge multiple VCF files (same variants, same sample) into one VCF file
... 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 trausch730

Latest awards to trausch

Appreciated 10 days ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 6 weeks ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 9 weeks ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 11 weeks ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 7 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 19 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 20 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 20 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?

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