User: trausch

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trausch1.0k
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Germany
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http://tobiasrausch.gi...
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1 day, 21 hours ago
Joined:
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Posts by trausch

<prev • 104 results • page 1 of 11 • next >
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Comment: C: repli-seq analysis pipeline
... It depends on the input BAMs. ...
written 19 days ago by trausch1.0k
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Comment: C: repli-seq analysis pipeline
... As far as I remember I used the normalization from [this paper][1]. [1]: http://www.pnas.org/content/107/1/139 ...
written 19 days ago by trausch1.0k
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Comment: C: repli-seq analysis pipeline
... I did create a very basic [Repli-Seq analysis workflow][1] a while ago. [1]: https://github.com/tobiasrausch/repliseq ...
written 23 days ago by trausch1.0k
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Answer: A: Splice junction sites and number of splitted reads from STAR aligned bam
... [Alfred][1] should work alfred count_jct -g Homo_spaiens.GRCh37.75.gtf.gz input.star.bam [1]: https://github.com/tobiasrausch/alfred ...
written 4 weeks ago by trausch1.0k
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Answer: A: ATAC-seq DE analysis
... Another ATAC-Seq pipeline is available [here][1]. As part of the pipeline a count matrix is generated and an Rscript template for differential peak calling is part of the pipeline ([script is here][2]). [1]: https://github.com/tobiasrausch/ATACseq [2]: https://github.com/tobiasrausch/ATACseq/b ...
written 5 weeks ago by trausch1.0k
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Comment: C: expected heterozygosity calculation
... Number of hets, hom. ref. and hom. alt. in a given region bcftools stats -r chr1:23000-26000 -s - You are probably interested in runs of homozygosity bcftools roh ...
written 8 weeks ago by trausch1.0k
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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 9 weeks ago by trausch1.0k
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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 9 weeks ago by trausch1.0k
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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 10 weeks ago by trausch1.0k
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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 10 weeks ago by trausch1.0k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 8 weeks 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 9 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?
Scholar 6 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 6 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 6 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 6 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 9 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
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 11 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
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 12 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 12 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 17 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.5 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 2.5 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.5 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144

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