User: trausch
trausch • 1.5k
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Posts by trausch
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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 9 weeks ago by
trausch • 1.5k
1
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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 9 weeks ago by
trausch • 1.5k
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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 4 months ago by
trausch • 1.5k
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3
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290
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... bcftools stats -s - | grep "^PSC"-B 1 ...
written 4 months ago by
trausch • 1.5k
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... 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
trausch • 1.5k
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1
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3.0k
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1
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... Updated the link. The section about delly is "SV Calling" ...
written 6 months ago by
trausch • 1.5k
1
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1
answer
360
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... [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
trausch • 1.5k
1
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1.4k
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... 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
trausch • 1.5k
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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
trausch • 1.5k
0
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2
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232
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... 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
trausch • 1.5k
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For A: Program to calculate and add the NM tag to a bam file
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For A: Program to calculate and add the NM tag to a bam file
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For A: Program to calculate and add the NM tag to a bam file
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: Get trace data for all four bases from ab1 file
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: Methods of classifying, not detecting, structural variation?
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For A: Methods of classifying, not detecting, structural variation?
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For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
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For A: Methods of classifying, not detecting, structural variation?
Good Answer
2.5 years ago,
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For A: Get trace data for all four bases from ab1 file
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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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