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In /project/evolgen/assem/alf1GBS_NS1_mar21/demulitplex I …
Also, the MID to sample name files didn’t follow the scheme we have used for GBS: MIDname, MID, sample id. Also, we don’t want the header. So, I made a fixed version (now we have Hmax1Demux_fixed.csv):
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tail -n+2 Pool1Alf1GbsTest_Demux.csv | sed -E 's/^([._[:alnum:]-]+),([._[:alnum:]-]+),([._[:alnum:]-]+).*/\3,\1,\2/' > Pool1Alf1GbsTest_Demux_fixed.csv
tail -n+2 Pool2Alf1GbsTest_Demux.csv | sed -E 's/^([._[:alnum:]-]+),([._[:alnum:]-]+),([._[:alnum:]-]+).*/\3,\1,\2/' > Pool2Alf1GbsTest_Demux_fixed.csv
tail -n+2 Pool3Alf1GbsTest_Demux.csv | sed -E 's/^([._[:alnum:]-]+),([._[:alnum:]-]+),([._[:alnum:]-]+).*/\3,\1,\2/' > Pool3Alf1GbsTest_Demux_fixed.csv
tail -n+2 Pool4Alf1GbsTest_Demux.csv | sed -E 's/^([._[:alnum:]-]+),([._[:alnum:]-]+),([._[:alnum:]-]+).*/\3,\1,\2/' > Pool4Alf1GbsTest_Demux_fixed.csv |
On I started parse_barcodes_slurm_pool1.sh etc (one for each pool) . Note that I did not do separate contaminant filtering (which I did for Penstemon), because the parsing code and other downstream steps should knock out contaminants. I can double-check this.