Daniel:Notebook/GenomeMiner/2013-10-7
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HL155 Novoalign
V4S1
Rerunning v4s1 novoalign (which did not finish the first time around). I used too large a fastq which requires way too much time. So I've adapted, and realized for v4s1 I only need index 13 from lane 2.
Novoalign
novoalign -d index_v4s1fullrevcomp.ndx -f ../../hl155_indx10to13.fq -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s1.sam
Convert to Bam and Sort
samtools view -bS novo_v4s1.sam | samtools sort - novo_v4s1_sort