User: trausch
trausch • 1.5k
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Posts by trausch
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... 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
trausch • 1.5k
0
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... 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
trausch • 1.5k
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... 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
trausch • 1.5k
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... [readfq][1] supports reading FASTA and FASTQ in various programming languages (incl python).
[1]: https://github.com/lh3/readfq ...
written 16 days ago by
trausch • 1.5k
1
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1.1k
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... 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
trausch • 1.5k
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... 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
trausch • 1.5k
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... 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
trausch • 1.5k
1
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2
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... 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
trausch • 1.5k
0
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6
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17k
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6
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... [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
trausch • 1.5k
0
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3
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672
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... bcftools stats -s - | grep "^PSC"-B 1 ...
written 11 months ago by
trausch • 1.5k
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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