Daniel:Notebook/GenomeMiner/2013-10-3
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HL155
Novoalign on HL155 (Started 10/02/2013)
Concatenate fq files into 1
cat s_2_1_Indx11.txt s_2_1_Indx12.txt s_2_1_Indx13.txt s_3_1_Indx10.txt s_3_1_Indx11.txt s_3_1_Indx12.txt > hl155_indx10to13.fq
Novoalign on V4S1
novoalign -d index_v4s1fullrevcomp.ndx -f ../../hl155_indx10to13.fq -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s1.sam