User: trausch

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trausch1.2k
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http://tobiasrausch.gi...
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Posts by trausch

<prev • 128 results • page 1 of 13 • next >
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Comment: C: Validate PCR DNA primers against whole de novel genome
... No publication yet, there is only the [GitHub README][1]. But I am happy to help if you encounter problems with dicey. Just open an issue in the repo. [1]: https://github.com/gear-genomics/dicey/blob/master/README.md ...
written 11 days ago by trausch1.2k
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Answer: A: Validate PCR DNA primers against whole de novel genome
... [Dicey][1] can do this. You first need to build an FM-Index and the standard FASTA index of your genome `dicey index -o new_genome.fa.fm9 new_genome.fa.gz` `samtools faidx new_genome.fa.gz` Then you can search primer pairs across the entire genome. `echo -e ">Primer_forward\nGCCCCATAGGTTTTGAA ...
written 11 days ago by trausch1.2k
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Answer: C: Exome Seq tutorial
... Our [Cancer Genomics/Rare Disease Tutorial][1] has a section on variant calling and quality control for whole-exome sequencing data. [1]: https://tobiasrausch.gitbooks.io/variant-calling/content/ ...
written 4 weeks ago by trausch1.2k
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Answer: A: VariantCalling with single sanger read
... Indigo outputs a BCF file with variant calls for Sanger sequencing: [https://gear.embl.de/indigo/][1] [1]: https://gear.embl.de/indigo/ ...
written 5 weeks ago by trausch1.2k
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Answer: A: Merging peak files for unionized set
... I am not sure if that's necessarily the best solution but we indeed use bedtools merge to get a unified peak list, then count fragments for each sample at these peaks and then run differential peak calling.Here is the link to our ATAC-Seq workflow: [https://github.com/tobiasrausch/ATACseq][1] [1 ...
written 6 weeks ago by trausch1.2k
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Comment: C: Where can I get the ab1 Peak Reporter tool
... We do have ab1 variant calling in Indigo [https://gear.embl.de/indigo/](https://gear.embl.de/indigo/) maybe that solves your problem? ...
written 8 weeks ago by trausch1.2k
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Comment: C: Get genotype GT from multi-sample VCF (per chromosome)
... I guess, he could just split and then cut away the first column. bcftools query -f '%CHROM[\t%GT]\n' | awk '{print $0 >> "chrom"$1".bed"}' ...
written 3 months ago by trausch1.2k
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Answer: A: Get genotype GT from multi-sample VCF (per chromosome)
... bcftools query should work. bcftools query -H -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT]\n' ...
written 3 months ago by trausch1.2k
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Comment: C: find coverage of specific exomes from a bam file
... Osx builds are skipped for performance reasons in the Bioconda versions, linux-64 is the default platform. You can either build from source on osx (requires boost library) or use [this minimal docker container of Alfred][1] (if you are familiar with docker). [1]: https://hub.docker.com/r/trausch/ ...
written 4 months ago by trausch1.2k
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Answer: A: find coverage of specific exomes from a bam file
... [Alfred][1] can be used for that: alfred count_dna -i exome.bed.gz -o coverage.gz input.bam [1]: https://github.com/tobiasrausch/alfred ...
written 4 months ago by trausch1.2k

Latest awards to trausch

Scholar 6 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Centurion 9 months ago, created 100 posts.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 14 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
Appreciated 14 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 14 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 18 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 19 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?
Appreciated 20 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 20 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.1 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 3.1 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 3.1 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144

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