Daniel:Notebook/GenomeMiner/2013-10-7: Difference between revisions

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>Djacobse
(Created page with "=HL155 Novoalign= Back to Calendar ==V4S1== Rerunning v4s1 novoalign (which did not finish the first time around). I used too large a fastq...")
 
>Djacobse
 
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'''Novoalign'''
'''Novoalign'''
  novoalign -d index_v4s1fullrevcomp.ndx -f ../../hl155_indx10to13.fq -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s1.sam
  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

Latest revision as of 17:43, 10 October 2013

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