Daniel:Notebook/GenomeMiner/2013-10-2

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HL155[edit]

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Novoalign Sequence Alignment[edit]

Running novoalign on the sequencing data from HL155 since novoalign seems to be the best alignment software (detects errors most correctly). Working off Matt's previous methods.

Build Index

novoindex index_v4s1fullrevcomp.ndx V4S1_fullrevcomp.fa

Run Novoalign

nohup novoalign -d index_v4s1fullrevcomp.ndx -f ../../s_2_1_Indx11.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s1_s21indx11.sam &

Issue here is that novoalign only runs on 1 fq at a time (I think). I'm going to see if I can cat the fq files before running.