seqex recipes

In the examples below I either show a generic name for an input file (ASSEMBLY.hdf5) when demonstrating options where I do not show example results, or I use SRP021469/OUT/assembly.hdf5 as the input file when using an example database file from the empirical SE denovo assembly tutorial.

windows (reference)

The -w/--windows argument can be used to specify one or more specific scaffolds/chromosomes by name from which you want to extract filtered loci to concatenate.

ipyrad2 seqex \
  -d ASSEMBLY.hdf \
  -o SEQEX \
  -w CHROM_01 \
  -C

You can use regular expression to select multiple scaffolds

ipyrad2 seqex \
  -d ASSEMBLY.hdf \
  -o SEQEX \
  -w CHROM_0[1-5] \
  -C

Or to select multiple scaffolds you can list them manually

ipyrad2 seqex \
  -d ASSEMBLY.hdf \
  -o SEQEX \
  -w CHROM_01 CHROM_02 CHROM_03 CHROM_04 CHROM_05 \
  -C

Or you can enter a BED formatted file

ipyrad2 seqex \
  -d ASSEMBLY.hdf \
  -o SEQEX \
  -w WINDOWS.bed \
  -C

min-samples-locus

Selected a subset of loci is less straight forward when working with a denovo assembly. Here the locus numbers are not very meaningful, except that subcomponent numbering indicates likely relationships of paralogs.

Let's say you wanted to sample 1000 random loci that meet your filtering requirements. You could do...

ipyrad2 seqex \
  -d SRP021469/OUT/assembly.hdf5 \
  -o SRP021469/output-seqex \
  -N 1000 \
  -C

imap/minmap

ipyrad2 seqex \
  -d SRP021469/OUT/assembly.hdf5 \
  -o SRP021469/output-seqex \
  -n assembly_min8 \
  --imap IMAP.tsv \
  --minmap MINMAP.tsv \
  -C