User: trausch
trausch • 1.4k
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Posts by trausch
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... I am not sure I fully understand your question. If you want all primer binding sites and possible amplicons across a genome for your multiplexed qPCR design then this tool should work: [https://www.gear-genomics.com/silica/][1]
[1]: https://www.gear-genomics.com/silica/ ...
written 13 days ago by
trausch • 1.4k
0
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... [Cibersort][1] could be an option.
[1]: https://www.nature.com/articles/nmeth.3337 ...
written 3 months ago by
trausch • 1.4k
3
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... Usually the insert size (fragment size) is small for WES. To avoid a lot of overlapping reads that are not independent observations we usually sequence only 2x75bp on a NextSeq. ...
written 3 months ago by
trausch • 1.4k
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... You can use [tracy][1] to patch a reference using Sanger sequences. It's a reference-guided algorithm to assemble Sanger traces and it also creates a consensus sequence.
tracy assemble -r reference_slice.fa forward.ab1 reverse.ab1
[1]: https://github.com/gear-genomics/tracy ...
written 3 months ago by
trausch • 1.4k
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Answer:
A: Export Coverage on IGV
... We first create coverage tracks in UCSC bedgraph format using [alfred][1]
alfred tracks -o sample1.bedGraph.gz sample1.bam
and then you can use [igvtools][2] to convert the bedGraph files to IGV's proprietory tdf format.
igvtools totdf sample1.bedGraph.gz sample1.tdf hg19
You can then ea ...
written 4 months ago by
trausch • 1.4k
1
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... The [kent utils][1] from the UCSC genome browser have a rapid tool for this
faCount -dinuc genome.fa
Precompiled binaries are [here][2].
[1]: http://hgdownload.soe.ucsc.edu/admin/exe/
[2]: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ ...
written 5 months ago by
trausch • 1.4k
1
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3
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3.4k
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... The InDel size doesn't matter as discussed in this Alfred [issue][1].
[1]: https://github.com/tobiasrausch/alfred/issues/3 ...
written 5 months ago by
trausch • 1.4k
1
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1
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... [Alfred][1] calculates the reference GC, target region GC and sample GC content. [Here][2] is an example, just select "DNA-Seq, Exome" from the reference data set collection and then jump to "GC Content". Command should be:
alfred qc -b targets.bed -r genome.fa -o out.stats.tsv.gz -j out.stats. ...
written 5 months ago by
trausch • 1.4k
0
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1
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Comment:
C: Oxford Nanopore error rate?
... As part of [HGSVC][1] one sample was sequenced with Oxford Nanopore (~1.5 years ago). You can browse the QC information of that sample [here][2], just select "DNA-Seq, Oxford Nanopore" from the set of reference data sets. The "Summary stats" tab lists the error rates of this data set for mismatches, ...
written 5 months ago by
trausch • 1.4k
2
votes
1
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264
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... For your downstream analyses you probably want to know how many exons (targets) are above a certain coverage threshold. In other words, you want to plot the fraction of targets >= X and then iterate X from 1x, 2x, ..., 50x coverage. In addition, you want to look at the on-target rate, i.e., how e ...
written 5 months ago by
trausch • 1.4k
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