User: trausch

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trausch1.5k
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Posts by trausch

<prev • 159 results • page 1 of 16 • next >
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Comment: C: Structural variants detection from assembled genome from Nanopore sequence data
... That's a matter of the assembly quality. If you have low coverage data you may also want to try mapping-based SV discovery approaches such as [Sniffles][1] or [delly][2] for [long-reads][3]. [1]: https://github.com/fritzsedlazeck/Sniffles [2]: https://github.com/dellytools/delly [3]: https:// ...
written 8 hours ago by trausch1.5k
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Answer: A: Structural variants detection from assembled genome from Nanopore sequence data
... There are multiple options, [mingraph][1] for instance has [SV calling][2] or [pav][3]. [1]: https://github.com/lh3/minigraph [2]: https://github.com/lh3/minigraph#calling-structural-variations [3]: https://github.com/EichlerLab/pav ...
written 8 hours ago by trausch1.5k
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Answer: A: Sanger sequencing chromatogram aligned to reference gene
... Indeed, you can use [tracy][1] as a command-line application to process them in batch or use the online web applications: * Trace alignment: [https://www.gear-genomics.com/sage/][2] * Variant calling: [https://www.gear-genomics.com/indigo/][3] * Multiple trace alignment (reference-guided or de novo ...
written 7 days ago by trausch1.5k
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Answer: A: How to parse a .fasta file in python ?
... [readfq][1] supports reading FASTA and FASTQ in various programming languages (incl python). [1]: https://github.com/lh3/readfq ...
written 16 days ago by trausch1.5k
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Answer: A: What are the strands of structural variant breakpoints?
... I am not sure about other tools but [delly][1] outputs INFO/CT which captures the orientation of SV breakpoints. The mapping of SV breakpoints to potential fusion genes is explained [here][2]. [1]: https://github.com/dellytools/delly [2]: https://github.com/dellytools/sansa#discovering-gene-fus ...
written 7 weeks ago by trausch1.5k
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Answer: A: 1000 Genome Project Structural Variants for Illumina
... These SV calls are based on illumina data and GRCh37: [http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/][1] The GRCh38 subdirectory are the lifted SV calls. [1]: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ ...
written 3 months ago by trausch1.5k
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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 8 months 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 8 months 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 11 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 11 months ago by trausch1.5k

Latest awards to trausch

Teacher 7 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 9 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 10 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 12 months ago, created an answer that has been accepted. For A: Cosmic mutation signature
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
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?
Good Answer 14 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 17 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 18 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 2.4 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Centurion 2.6 years ago, created 100 posts.
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 2.7 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 2.7 years ago, received more than 100 upvotes.
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 3.0 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 3.0 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 3.0 years ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 3.0 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144

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