User: trausch

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trausch1.3k
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http://tobiasrausch.gi...
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Posts by trausch

<prev • 139 results • page 1 of 14 • next >
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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 5 days ago by trausch1.3k
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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 17 days ago by trausch1.3k
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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 6 weeks ago by trausch1.3k
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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 6 weeks ago by trausch1.3k
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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 7 weeks ago by trausch1.3k
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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 8 weeks ago by trausch1.3k
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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 9 weeks ago by trausch1.3k
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Answer: A: Generating consensus sequence from bam file
... [Alfred][1] has a consensus mode that extracts all reads at a given alignment position and then runs a multiple sequence alignment computation with consensus generation. It's primarily for long reads but I think it also works for short reads. alfred consensus -t ill -f bam -p chr4:500500 input. ...
written 10 weeks ago by trausch1.3k
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Comment: C: DELLY CNV Calling
... Yes, everything except Chr17. You can just list them all line-by-line: chr1 chr2 ... chr16 chr18 chr19 ... ...
written 3 months ago by trausch1.3k
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Answer: C: ATAC-seq : which read length?
... My suggestion would be to sequence in paired-end mode at short read length (50 or 75bp is fine but not longer) because then the insert size is informative for nucleosome patterns and you have more options for footprint analyses. ...
written 4 months ago by trausch1.3k

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Appreciated 11 days ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 10 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Centurion 13 months ago, created 100 posts.
Teacher 13 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
Guru 14 months ago, received more than 100 upvotes.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 18 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 18 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 18 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 18 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 22 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 23 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.0 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 2.0 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.5 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 3.5 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144

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