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If I generated a VCF file for a trio (with a father using deeptrio) or a solo male (using deepvariant) without --haploid_contigs="chrX,chrY" and/or --par_regions_bed parameters. Can I fix the VCF afte…
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"In terms of diagnostic terms for prenatal medicine, I took a look at the second link. Some ideas:
- [x] Imaging modalities used in the prenatal setting include both ultrasound (including echocardiog…
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We noticed a strong drop in precision for SNVs (~10% for tumor-normal mode, ~20% in tumor-only mode) between releases 4.1.7.0 and 4.2.6.0.
With more testing using the HCC1395 somatic benchmark (https…
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"Targeted sequencing for the full coding sequence of 69 genes and genomewide copy-number information was undertaken in 1887 patients"
PMID: 30304655
https://www.ncbi.nlm.nih.gov/pubmed/30304655
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jjgao updated
4 months ago
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Hi, thanks for developing such a useful tool!
Our lab is interested in applying the Optimized 10x method to AML scRNA-seq samples we already sequenced as part of a [recent publication](https://www.…
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I am also trying to combine two count matrices from the same sample (same 10x 3' platform) but for the second sequencing i ordered a fully custom panel of baits (only containing 50 genes of interest) …
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Hi!
I have read the [previous question](https://github.com/HadrienG/InSilicoSeq/issues/95) regarding the enhancement of InSilicoSeqs for simulating reads for targeted amplicon sequencing. Is this f…
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I have been attempting to build a GPC cross-compiler (h8300-hitachi-coff) but thus far have been unsuccessful. Without GPC, I can successfully build binutils, gcc (including language support for C, C…
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I have output from multiple sequencing runs that I want to analyze together, and some data from the same sequencing runs that I want to analyze separately. So my questions are:
1) should I combine da…
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Hello, I am interested in starting using TRUST4, and was wondering what is the best approach to run it on SMARTer data, in terms of parameters, pre-processing, etc.
I run a subset of 100K paired-en…