User: trausch

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trausch1.4k
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Germany
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http://tobiasrausch.gi...
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Posts by trausch

<prev • 142 results • page 1 of 15 • next >
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Answer: A: Checking quality of predesigned probes for multiplex qPCR
... 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 trausch1.4k
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Answer: A: Options for cell type deconvolution from whole blood?
... [Cibersort][1] could be an option. [1]: https://www.nature.com/articles/nmeth.3337 ...
written 3 months ago by trausch1.4k
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Answer: A: number of cycles, Nextseq500, for whole exoems equencing, which option is more e
... 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 trausch1.4k
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Answer: A: How to align paired-end Sanger sequences
... 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 trausch1.4k
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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 trausch1.4k
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Answer: A: Calculating dinucleotide frequencies for each sequence in a multi fasta file
... 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 trausch1.4k
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Comment: C: Mismatch and Indel statistics from BAM/SAM file
... 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 trausch1.4k
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Answer: A: Graphing GC Bias in Sequence Capture
... [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 trausch1.4k
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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 trausch1.4k
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Answer: A: Comparing metrics of two exome: how to interpret higher median coverage but lowe
... 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 trausch1.4k

Latest awards to trausch

Good Answer 23 hours ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
Scholar 3 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 4 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 14 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Centurion 17 months ago, created 100 posts.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
Guru 17 months ago, received more than 100 upvotes.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 21 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
Appreciated 22 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 22 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 2.3 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.3 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length

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