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Questions: 1. In analyzing an assembly made from diploid DNA using Illumina reads from haploid DNA (a meiotic product from the diploid individual), should ploidy be set to one or two for Merfin? 2. If…
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**Describe the issue with the metadata**
It is not clear from the definition exactly what is desired for the readDepth column. Is this the total number of reads? The coverage ("Lander/Waterman equati…
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Hi there,
I have a reference imputation panel with indels, but followed the tutorial so created a sites.tsv and site.vcf without those indels but the reference panel still has them. I thought GLIMP…
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Hi! If there is a way I can know which raw reads go to a specific contig?
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The command I use is as follows：
run_clair3.sh \
--ref_fn=/home/gyc/ont/seq/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
--bam_fn=/home/gyc/ont/fast5/workspace/output/out166/std/out.bam \
--t…
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I noticed a difference in behaviour when reconstructing using vcf or a fasta alignment for ambiguous bases. In the resulting nexus the ambiguous bases in samples are labelled as changes to reference i…
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Hi, Dr. Lovell. I ran analysis and I got this error:
##############
Flagging over-dispered OGs
...amphioxus: 2048 genes in 99 OGs hit > 8 unique places ***
...chicken : 246 genes in 8 OG…
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We've been using breseq for calling individual samples from a longitudinal study, but have run into issues when comparing results from multiple samples. This seems to partly be a threshold effect, wh…
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Hi, I'm trying to convert the UK Biobank 200k Whole Exome Sequencing dataset to a single plink2 dataset:
```bash
#> plink2 --pmerge-list mergelist.txt --out /s/project/uk_biobank/processed/WES_200K/…
Hoeze updated
2 years ago
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I'm using strataG (v2.5.01; R version 4.2.0) to run fastSimcoal2 simulations (with DNA markers) and convert the Arlequin outputs to gtype objects. However, when I run `fsc2gtypes` on my fsc parameters…