User: trausch

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trausch890
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890
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Germany
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http://tobiasrausch.gi...
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1 week, 5 days ago
Joined:
2 years, 8 months ago
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Posts by trausch

<prev • 90 results • page 1 of 9 • next >
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Comment: C: Calculating coverage on a list of individual genes in WES data?
... I recently added cram support. If you clone the github repository there is an example [Rscript][1] that downloads ccds genes from UCSC and stores all exons in a BED file. [1]: https://github.com/tobiasrausch/alfred/blob/master/exon/exon.R ...
written 18 days ago by trausch890
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Answer: A: Calculating coverage on a list of individual genes in WES data?
... If you want a fragment count table for these genes you can use [Alfred][1]: alfred count_dna -o cov.tsv.gz -i genes.bed For estimating the on-target rate and the avg. coverage per target region: alfred qc -b genes.bed -o qc.tsv.gz -r Static binaries are available [here][2] or via [Bio ...
written 19 days ago by trausch890
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Answer: A: How to get counts data for allele specific expression analysis (ASE) from aligne
... You may want to try [Allis][1]. It requires an RNA-Seq BAM and optionally variant calls from WGS or WES. If no variants are provided they are called from the RNA-Seq BAM file. The variants are then phased against the 1000 Genomes reference panel (hg19) using [Eagle2][2]. [Allis][3] then parses the ...
written 28 days ago by trausch890
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Answer: A: Number of individuals in 1000genomes superpopulations?
... http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel ...
written 29 days ago by trausch890
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Answer: A: Primer design to do qPCR on repetitive elements
... [Silica][1] can check primers genome-wide. It uses the same thermodynamic calculations as [Primer3][2] and outputs all primer binding sites and possible amplicons. For a repetitive element it's probably a bit back and forth of designing new primers using slightly different parameters and checking th ...
written 5 weeks ago by trausch890
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Comment: C: Get trace data for all four bases from ab1 file
... If you look at the basenum column it should go from 1 to 434. The trace is longer, all called peaks have a basenum value. In the GUI the x-ticks correspond to the basecall positions. ...
written 5 weeks ago by trausch890
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Answer: A: Get trace data for all four bases from ab1 file
... [Teal][1] can do this. ./teal The tab-delimited output file lists the trace with the basecalls. There is also an [online method][2] to visualize the trace on [GEAR][3]. [1]: https://github.com/gear-genomics/teal [2]: https://gear.embl.de/teal [3]: https://gear.embl.de/ ...
written 5 weeks ago by trausch890
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Answer: A: Do I need to provide the Illumina's target region bed file for qualimap?
... I don't have any experience with qualimap but the on-target rate and the targeted sequencing coverage can also be computed by [Alfred][1] (disclaimer: my own tool). [1]: https://github.com/tobiasrausch/alfred ...
written 6 weeks ago by trausch890
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Comment: C: comparison of exome data to the 1000Genomes WGS data
... Thanks, so this is a population VCF with >10,000 samples? Then the callset is dominated by rare alleles such as singletons and doubletons of allele count 1 and 2. If you subset your VCF to common variants (MAF>1%) you will have a large intersection with 1000 Genomes and for the rare ones it is ...
written 3 months ago by trausch890
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Comment: A: comparison of exome data to the 1000Genomes WGS data
... 300,000 SNPs on chr1 for an exome capture data set? We usually have <100,000 confident exonic SNPs across the whole-genome for whole-exome sequencing. What is the on-target rate and the fraction of targets >=30x? ...
written 3 months ago by trausch890

Latest awards to trausch

Scholar 29 days ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 5 weeks ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 5 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 6 months 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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 7 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 7 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 12 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.0 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 2.1 years 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
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?

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