bensutherland/nano2geno

Genotyping from nanopore data

nano2geno's Issues

Make a log file output folder for de-multiplexing result output info

Need to be able to retain information after de-multiplexing. Add a date stamp. See stacks_workflow for demo.

Persistent issue with carry over of 3 digid locations

Grep in 04_select_variants.sh continues to print all three digit locations representing 2 digit search parameter.
E.g.:
"Oki104569261.312_312 Oki104569261.312 312 G 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
Ots_crRAD44016.74_74 Ots_crRAD44016.74 74 T 5 0 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0
Ots_crRAD52613.29_290 Ots_crRAD52613.29 290 C 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
Ots_crRAD52613.29_291 Ots_crRAD52613.29 291 C 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
Ots_crRAD52613.29_292 Ots_crRAD52613.29 292 T 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
Ots_crRAD52613.29_293 Ots_crRAD52613.29 293 G 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
Ots_crRAD52613.29_294 Ots_crRAD52613.29 294 A 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
Ots_crRAD52613.29_295 Ots_crRAD52613.29 295 C 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
Ots_crRAD52613.29_296 Ots_crRAD52613.29 296 A 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
Ots_crRAD52613.29_297 Ots_crRAD52613.29 297 G 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
Ots_crRAD52613.29_298 Ots_crRAD52613.29 298 G 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
Ots_crRAD52613.29_299 Ots_crRAD52613.29 299 T 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
"

Library demultiplexing workflow

Current workflow doesn't differentiate downstream workflow after library de-multiplexing. Thus, the second library fish ID barcode demultiplexing would overwrite the first library fish ID barcode results.

Do the first de-multiplex without discarding reads with middle adapters

Binning discards reads with middle adapters by default.
Porechop is currently seeing 96 or 95 barcodes internally, e.g. when multiple external library adapter segments are ligated together.
Do porechop without binning, without trimming, with only splitting.
Then do porechop w/ binning+trimming (and shouldn't lose any reads based on internal adapters.

Calling heterozygotes

Currently can't differentiate between heterozygous and homozygous hotspots.

Underscores in sample names

Noticed a small issue in: https://github.com/bensutherland/nano2geno/blob/master/01_scripts/05_run_collect_select_genos.sh

sample=$( basename $file | awk -F_ '{ print $1 }' - )

is a problem when the sample name has an "underscore" in it (eg. BC01_n*). Probably need to ban underscores in the sample name, or use another way to get the variable here. Given that the for loop is predicated on "_var_w_index_selected.txt" , it might make more sense to replace that portion of the text instead - sed maybe?

sample=$( basename $file | sed 's/_var_w_index_selected.txt//g' - )

Might be a more efficient way, but seemed to work for me