User: trausch

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trausch1.1k
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Germany
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http://tobiasrausch.gi...
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Posts by trausch

<prev • 120 results • page 1 of 12 • next >
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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 2 days ago by trausch1.1k
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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 6 days ago by trausch1.1k
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Answer: A: Majority consensus from bam file
... This should work using [Alfred][1] ./alfred consensus -f bam -t ont -p chr1:218992200 The alignment scoring depends on the sequencing technology. If you have phased SNPs and long reads you should split the BAMs into haplotypes prior to the consensus computation. [1]: https://github.com/tob ...
written 4 weeks ago by trausch1.1k
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Comment: C: Other then picard better way to calculate insertmetrics from a bam file ?
... Thanks, did alfred work? ...
written 6 weeks ago by trausch1.1k
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Answer: A: Other then picard better way to calculate insertmetrics from a bam file ?
... Another option is [Alfred][1]. We provide example quality control files for different sequencing assays (DNA-Seq whole-exome, ATAC-Seq, ...) and different sequencing technologies (Illumina, ONT, PacBio) at the [companion web application][2] so you can have a look if that's what you are looking for ( ...
written 6 weeks ago by trausch1.1k
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Answer: A: DNA sequences from the origins of replication.
... [Repli-Seq][1] can be used to map origins of replication. For humans there are likely cell-type-specific replication programs. [1]: http://www.pnas.org/content/107/1/139 ...
written 6 weeks ago by trausch1.1k
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Answer: A: Human CNV VCF for Trios from whole-genomes
... [Delly][1] SV calls for the [HGSVC trios][2] are available [here][3]. [1]: https://github.com/dellytools/delly [2]: https://www.biorxiv.org/content/early/2018/06/13/193144 [3]: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/hgsv_sv_discovery/working/20160930_pre_ashg_calls/2016100 ...
written 9 weeks ago by trausch1.1k
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Comment: C: Identification of break points for a balanced translocation
... You can just extract the 2 translocated chromosomes of interest: samtools view -b chrA chrB > subset.bam samtools index subset.bam Or if you know the approximate regions: samtools view -b chrA:10000000-20000000 chrB:50000000-60000000 > subset.bam samtools index subset.bam ...
written 9 weeks ago by trausch1.1k
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Answer: A: Identification of break points for a balanced translocation
... If you have paired-end whole genome data you can use [Delly][1]. [1]: https://github.com/dellytools/delly ...
written 9 weeks ago by trausch1.1k
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Answer: A: Software to analyse mutations in sanger sequencing files
... [Indigo][1] is open-source. Indigo analyses sanger sequencing files (ab1), separates het. InDel mutations and aligns the sequences to a reference genome, wildtype chromatogram or custom fasta file. It also works for homozygous mutations or SNP identification in general. [1]: https://gear.embl.de/ ...
written 10 weeks ago by trausch1.1k

Latest awards to trausch

Scholar 9 weeks ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Centurion 4 months ago, created 100 posts.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
Guru 5 months ago, received more than 100 upvotes.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
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
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
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
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 14 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 15 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 16 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 16 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 16 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 21 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.8 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 2.8 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144

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