User: serpalma.v

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serpalma.v20
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Germany
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Posts by serpalma.v

<prev • 64 results • page 1 of 7 • next >
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Comment: C: How to select SNPs the most conservative way after WGS Variant Calling?
... Thanks Istvan OK, I will call variants with SAM/BCFtools on the same BAMs as well. Then I can subset both raw call sets by depth and allele frequency. Then consider common intersecting SNPs as the good ones. To filter by depth, I guess that I could only take the SNPs where all samples have a dept ...
written 7 days ago by serpalma.v20
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How to select SNPs the most conservative way after WGS Variant Calling?
... Hello! I have made a raw (unfiltered) variant call set following GATK best practices (VCF file with ~16 Million SNPs produced by GenotypeGVCFs). The original WGS data corresponds to 60 samples sequenced at a average coverage of 20x. We want to identify a small subset of really good SNPs and anothe ...
next-gen snp sequencing written 8 days ago by serpalma.v20 • updated 8 days ago by Istvan Albert ♦♦ 79k
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Comment: C: Best tool for variant calling
... What is the purpose of passing the BAM and subsets thereof? Would that be necessary if I have, for instance, 10 BAMs from different samples? Thanks ...
written 9 days ago by serpalma.v20
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Comment: C: Overrepresented stretches of Gs in NovaSeq library
... After checking the literature, I found two softwares that address, among other things, the poly-G problem: [AfterQC][1] and [fastp][2]. Both from the same author, and the later is faster than the former. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374548/ [2]: https://academic.oup.com/b ...
written 24 days ago by serpalma.v20
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Comment: C: what cause poly-G from NextSeq
... what is better to remove adapters, quality and poly-G filtering: `AfterQC` or `fastp`? ...
written 24 days ago by serpalma.v20
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Comment: C: Overrepresented stretches of Gs in NovaSeq library
... Thanks Michael, is there a tool that you would recomend to do the job? I am not sure if `trimmomatic` is the right tool for this. Thanks ...
written 24 days ago by serpalma.v20
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Overrepresented stretches of Gs in NovaSeq library
... `FastQC` reports in the `overrepresented sequences` module a warning for all R2 FASTQ's corresponding to a stretch of >50 G's, amounting to <0.5% and <0.3% of the whole library before and after removing of adapters (TrueSeq Nano), respectively. Our partner that performed the labwork advis ...
fastqc sequencing dna written 24 days ago by serpalma.v20 • updated 24 days ago by michael.ante3.0k
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Reference TiTv ratio for mouse WGS?
... Hello! I am wondering if anyone has a reference for the Ti Tv ratio in mouse WGS. I've gone through the literature but without much success except two publications. This [publication][1] calculates the TiTv ratio for het-SNPs (Ti=66.3%; Tv=33.7%) and hom-SNPs (Ti=77.7%; Tv=22.3%), which I interepr ...
mouse transversion transition snp titv written 5 weeks ago by serpalma.v20
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History of the mouse genome
... Hello! I am trying to understand the origin of the mouse genome because I just started working in this species and I want to have a good overview before going any further. I know that the original draft was the [MGSCv3 published in 2002][1]. Then came the so-called [built36 in 2009][2], [the MGSCv ...
genome mouse sequencing written 8 weeks ago by serpalma.v20 • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
... As I understand it, in order to be cosidered a bed file, the bed extension should be specified: > To indicate that a file be treated as BED rather than the 1-based tab-delimited file, the file must have the ".bed" or ".bed.gz" suffix (case-insensitive). Otherwise, the ``--regions-file`` is trea ...
written 9 weeks ago by serpalma.v20

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