Daniel:Notebook/GenomeMiner/2013-10-7

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HL155 Novoalign[edit]

Back to Calendar

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