User: trausch

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trausch1.5k
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Germany
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https://tobiasrausch.com/
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3 weeks, 2 days ago
Joined:
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Posts by trausch

<prev • 153 results • page 1 of 16 • next >
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Comment: C: How to compare Sanger Sequenced data to the reference sequence?
... If it is a commonly used model organism we can add the reference sequence to our set of pre-indexed genomes. If you are only interested in a single gene or exon the FASTA upload is indeed best. ...
written 9 weeks ago by trausch1.5k
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Answer: A: How to compare Sanger Sequenced data to the reference sequence?
... We developed open-source web applications to align Sanger chromatogram traces and call variants with respect to a reference genome. You can also do a reference-guided assembly: Alignment: [https://www.gear-genomics.com/sage/][1] Variant Calling: [https://www.gear-genomics.com/indigo/][2] Referenc ...
written 9 weeks ago by trausch1.5k
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Answer: A: Automated Primer-Blast like funcionnality
... [Silica][1] searches (multiple) PCR primers across entire genomes using primer3's thermodynamic calculations. It's an installation-free, open-source in-silico PCR web application: [https://www.gear-genomics.com/silica/][2] [1]: https://www.gear-genomics.com/silica/ [2]: https://www.gear-genomi ...
written 4 months ago by trausch1.5k
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Answer: A: how to estimate heterozygosity by sample from a multi-sample vcf file
... bcftools stats -s - | grep "^PSC"-B 1 ...
written 4 months ago by trausch1.5k
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Comment: C: bcftools view filter exclude not working when using logical operators
... I think, & and && have different meanings, see this [filtering tutorial][1]. [1]: http://samtools.github.io/bcftools/howtos/filtering.html ...
written 5 months ago by trausch1.5k
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Comment: C: Explain the definition of DELLY output
... Updated the link. The section about delly is "SV Calling" ...
written 6 months ago by trausch1.5k
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Answer: A: Illumina WES intervals file for coverage analysis?
... [ExAC][1] published an interval list of callable regions for WES. In our experience this interval list is pretty well covered by all exome capture kits (illumina, Agilent, ...) and thus, good for QC and coverage analysis purposes. Coordinates are hg19/GRCh37. There are plenty of tools to then calcul ...
written 6 months ago by trausch1.5k
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Answer: A: Sanger sequencing data analysis
... We recently developed [Tracy][1] to analyze Sanger sequencing data, works from the command-line and using [web applications][2]. [1]: https://github.com/gear-genomics/tracy [2]: http://www.gear-genomics.com/ ...
written 7 months ago by trausch1.5k
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Comment: C: Sanger sequencing data analysis
... The novoSNP URL appears to be dead. Is there an updated one? ...
written 7 months ago by trausch1.5k
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Answer: A: Fusion orientation make sense or not
... I think [snpEff][1] can annotate SVs from Delly and Manta in VCF format for potential gene fusions. [1]: http://snpeff.sourceforge.net/ ...
written 7 months ago by trausch1.5k

Latest awards to trausch

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Program to calculate and add the NM tag to a bam file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Program to calculate and add the NM tag to a bam file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Program to calculate and add the NM tag to a bam file
Scholar 6 months ago, created an answer that has been accepted. For A: Cosmic mutation signature
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
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
Scholar 11 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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 15 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 22 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Centurion 2.1 years ago, created 100 posts.
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
Guru 2.1 years ago, received more than 100 upvotes.
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 2.5 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?
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
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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