User: trausch

gravatar for trausch
trausch1000
Reputation:
1,000
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Location:
Germany
Website:
http://tobiasrausch.gi...
Scholar ID:
Google Scholar Page
Last seen:
11 hours ago
Joined:
2 years, 11 months ago
Email:
r*********@gmail.com

Posts by trausch

<prev • 98 results • page 1 of 10 • next >
2
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Comment: C: Add AF from 1000 genomes vcf file to a different vcf file
... bcftools annotate -a EUR.chr13.phase1.vcf.gz -c INFO/AF:=INFO/EUR_AF my_vcf > EUR_AF.vcf ...
written 3 days ago by trausch1000
3
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2
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115
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2
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Answer: A: Add AF from 1000 genomes vcf file to a different vcf file
... bcftools annotate -a EUR.chr13.phase1.vcf.gz -c INFO/AF ...
written 4 days ago by trausch1000
1
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0
answers
164
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0
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Comment: C: Weird insert size distribution
... I suspect your read-length is ~135bp? The insert size is usually the outward distance so the lower bound is the read-length. [Alfred][1] (disclaimer: my own tool) splits the insert size by all possible 4 types of read pair orientations so this will at least tell you if you have the standard illumina ...
written 12 days ago by trausch1000
1
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1
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90
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1
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Comment: C: calculate ti/tv ratio in WGS data
... The expected ratio of transitions to transversions in the whole genome is near 2.0 for humans. ...
written 13 days ago by trausch1000
1
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1
answer
90
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1
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Answer: A: calculate ti/tv ratio in WGS data
... bcftools stats snv.vcf.gz | grep "TSTV" ...
written 14 days ago by trausch1000
1
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4
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134
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4
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Answer: A: bam file to .bedgraph
... [Alfred][1] is another option: alfred tracks -o out.bedGraph.gz input.bam [1]: https://github.com/tobiasrausch/alfred ...
written 21 days ago by trausch1000
0
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1
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112
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1
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Answer: A: How to normalize the bam files for RNA-Seq samples for visualization
... Viewing multiple BAM files in IGV is a little slow. We developed [Alfred][1] which creates browser tracks and at the same time normalizes to ~30 million reads by default. The resolution parameter '-r' adjusts the file size of the browser track. The default of 0.2 usually results in a browser track o ...
written 4 weeks ago by trausch1000
0
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0
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188
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0
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Comment: C: SV detection software using split reads only?
... If you subset the [Delly][1] output to SV calls with the INFO:PRECISE flag then all these SVs are supported by split read information. [1]: https://github.com/dellytools/delly ...
written 11 weeks ago by trausch1000
0
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1
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293
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1
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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 3 months ago by trausch1000
1
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1
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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 3 months ago by trausch1000

Latest awards to trausch

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 4 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 4 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 4 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 4 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 8 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 9 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 10 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 10 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 10 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 15 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.3 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 2.3 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.3 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?

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