User: jean.elbers
jean.elbers • 450
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Posts by jean.elbers
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... I would use the most up-to-date Swiss-Prot database
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
and not worry about combining RefSeq or transposon sequences. Someone with more experience might have better advice to give, but I ...
written 17 hours ago by
jean.elbers • 450
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... Perhaps you could do SNP/indel calling by aligning the transcriptomic reads with an aligner such as [`BBMap`][1] (maybe using `mapPacBio.sh`) then calling variants with BBTools' `callvariants.sh`, then using `BCFtools` to get the consensus sequence?
[1]: https://sourceforge.net/projects/bbmap/ ...
written 19 hours ago by
jean.elbers • 450
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... If I understand you correctly, you have a .ped file with half-missing genotypes but cannot convert it to VCF using PLINK v. 1.9? If you have some example data to post, perhaps I could write a regular expression to convert the half-missing genotypes to missing genotypes (not making any promises, but ...
written 21 hours ago by
jean.elbers • 450
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... Try
HAYSData$Rep<-as.factor(paste(HAYSData$Rep))
...
written 2 days ago by
jean.elbers • 450
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... If this is what you would like to do, then I think for your purposes, you can simply do:
bbnorm.sh in=reads.fq out=normalized-30x.fq target=30 min=5
bbnorm.sh in=reads.fq out=normalized-20x.fq target=20 min=5
bbnorm.sh in=reads.fq out=normalized-10x.fq target=10 min=5
And then re-r ...
written 2 days ago by
jean.elbers • 450
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... I am not sure if you would like to downsample the reads to 30x, 20x, and 10x coverage or if you want parts of the genome that have 30x, 20x, and 10x coverage. If you are looking to downsample the reads, try bbnorm (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbnorm-guide/) ...
written 3 days ago by
jean.elbers • 450
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... ABySS offers a bloom filter (https://github.com/bcgsc/abyss#assembling-using-a-bloom-filter-de-bruijn-graph), so you could redo the assembly using the bloom filter to reduce memory usage. ...
written 4 days ago by
jean.elbers • 450
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... You can specify a custom repeat library (in FASTA format) with `rmlib` in the Repeat Masking section of the `make_opts.ctl` file
#-----Repeat Masking (leave values blank to skip repeat masking)
model_org=all #select a model organism for RepBase masking in RepeatMasker
rmlib=repeatlibrar ...
written 5 days ago by
jean.elbers • 450
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Answer:
A: Reference based assembly
... You might consider Reference-guided de novo assembly (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1911-6 ). Before trying though, you should read the paper and look at the improvement for each assembler in de novo versus reference-guided de novo mode. There is a convenien ...
written 6 days ago by
jean.elbers • 450
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... These appear to be very small N50 sizes and very large L50 sizes. Were these de novo assembled with only short-insert Illumina libraries (i.e., no long-insert [mate-pair] libraries for scaffolding were used in the ABySS assembly)? ...
written 18 days ago by
jean.elbers • 450
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For A: What is Read Group platform??
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For A: What is Read Group platform??
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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