Daniel:Notebook/GenomeMiner/2013-10-7
Jump to navigation
Jump to search
HL155 Novoalign[edit]
V4S1[edit]
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 ../../s_2_1_Indx13.txt -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
Filter
samtools view -h -F 4 -q 70 novo_v4s1_sort.bam > novo_v4s1_sortfilt.sam