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Follow up to #50
- [x] Meet with Wellington on Aug 2, document data description
- [x] Provide Wellington with list of files with missing dates and duplicate genotypes from site-year-block combinations…
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hello,I used the following command:
`bsub -o bo_canu_bsub_output.err canu -p bo_canu2 -d /gss1/home/yy20200615/bo_canu2 genomeSize=350m maxThreads=40 -pacbio rice.m64048_201207_040454.subreads.fast…
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Hi,
I'm having problems with canu not finding any overlaps during the mhap step. The dataset is nanopore reads basecalled using Guppy and the SUP model, adaptor-trimmed using porechop and filtered …
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Hi there,
I have been trying to run Canu 2.1.1 on some nanopore long reads using the script:
```
load_canu
canu gridOptions="-p safs" minThreads=48 -d /safs-data01/uqkweigh/long-read-assemblie…
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Running the following command with a phased **tetraploid** vcf and bam file with defined sample name in the RG field, the reads in the output bam are not tagged. To generate the bam, I've mapped the c…
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Hi Florian,
I have been transitioning from ldpred1 to ldpred2 and as a sanity check I have been running a set of analyses on the exact same datasets. The summary statistics are from the UK Biobank …
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Hi there,
When I use overlap_remove=TRUE with parallel windows, I get a subscript out of range error.
The process of overlap removal seems to complete:
Start_Overlap_removal:
Before: 174 Blo…
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In the meanwhile I did some testing with the `g360` models:
`medaka_variant -f scf1-10.fa -o r12-1 -s r941_prom_snp_g360 -m r941_prom_variant_g360 -t 10 -p -r 'OF1p3c_SSc_Bd_SSc_all_1:320000-520000' …
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I want to Run Canu on Lymphocyte cDNA to create full length Contigs for Downstream Analysis.
I ran Pychopper on a small subsample of the Run (21Mio Reads) to trim Primers and split Reads with middl…
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With the updates to find_ibd in #1637 it's now possible to reason about the IBD segments without having to explicitly convert them all to Python objects, removing a significant memory block. However,…