Daniel:Notebook/GenomeMiner/2013-10-7: Difference between revisions
Jump to navigation
Jump to search
>Djacobse (→V4S1) |
>Djacobse (→V4S1) |
||
Line 12: | Line 12: | ||
'''Convert to Bam and Sort''' | '''Convert to Bam and Sort''' | ||
samtools view -bS novo_v4s1.sam | samtools sort - novo_v4s1_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 |
Revision as of 23:35, 7 October 2013
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
Filter
samtools view -h -F 4 -q 70 novo_v4s1_sort.bam > novo_v4s1_sortfilt.sam