User: trausch

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

<prev • 114 results • page 1 of 12 • next >
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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 10 days 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 14 days 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 15 days 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 17 days ago by trausch1.1k
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Answer: A: calculate haloplex coverage
... We have used [Alfred][1] to calculate Haloplex on-target rate and target coverage distribution. `alfred qc -r -b ` [1]: https://github.com/tobiasrausch/alfred ...
written 18 days ago by trausch1.1k
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Answer: A: Normalising RNA-seq samples from bam files for UCSC Genome browser visualization
... [Alfred][1] (disclaimer: my own tool) can create UCSC browser tracks for paired-end RNA-Seq data alfred tracks -o ucsc.bedGraph.gz input.rna.bam The resolution parameter (-r) determines the file size (how aggressively coverage values are binned). By default, the method normalizes to ~30 millio ...
written 5 weeks ago by trausch1.1k
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Answer: A: AB1 to FASTQ
... [Tracy][1] can also convert to Fasta or Fastq: tracy basecall -o out.fastq -f fastq input.ab1 [1]: https://github.com/gear-genomics/tracy ...
written 5 weeks ago by trausch1.1k
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Answer: A: Detecting Homozygous Insertion from Sanger Seq
... You can decompose the Sanger trace using [Indigo][1]. It should work for het. and hom. indels. [1]: https://gear.embl.de/indigo ...
written 7 weeks ago by trausch1.1k
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Answer: A: RNA-seq : Quantification problem after mapped with BBMap
... I think, BBMap uses the new CIGAR characters = (sequence match) and X (sequence mismatch) and that might not be supported yet in your quantification methods. The latest version of [Alfred][1] v0.1.8 can handle these and also does RNA-Seq quantification: alfred count_rna -g Homo_sapiens.GRCh38.7 ...
written 7 weeks ago by trausch1.1k
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Comment: C: Explain the definition of DELLY output
... I updated the above link (I meanwhile extended the old Delly tutorial in a larger variant calling tutorial) ...
written 8 weeks ago by trausch1.1k

Latest awards to trausch

Scholar 14 days ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Centurion 3 months ago, created 100 posts.
Teacher 3 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
Guru 4 months ago, received more than 100 upvotes.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 8 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 8 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 8 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 8 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 11 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
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 13 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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?
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
Scholar 19 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.6 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 2.7 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144

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