Daniel:Notebook/GenomeMiner/2013-10-8: Difference between revisions
Jump to navigation
Jump to search
>Djacobse (→V4S2) |
>Djacobse |
||
(4 intermediate revisions by the same user not shown) | |||
Line 18: | Line 18: | ||
==V4S2== | ==V4S2== | ||
===Pipeline=== | |||
'''Build Index''' | '''Build Index''' | ||
Line 27: | Line 29: | ||
'''Convert to Bam and Sort''' | '''Convert to Bam and Sort''' | ||
samtools view -bS novo_v4s2.sam | samtools sort - novo_v4s2_sort | samtools view -bS novo_v4s2.sam | samtools sort - novo_v4s2_sort | ||
'''Filter''' | |||
samtools view -h -F 4 -q 70 novo_v4s2_sort.bam > novo_v4s2_sortfilt.sam | |||
'''Calmd''' | |||
samtools calmd -eS novo_v4s2_sortfilt.sam V4S2_fullrevcomp.fa > novo_v4s2_sortfilteq.sam | |||
'''Perl Error Counting Script''' | |||
perl count_mismatch.plx | |||
===Alignment Results=== | ===Alignment Results=== | ||
Line 39: | Line 50: | ||
# CPU Time: 179.1 (min.) | # CPU Time: 179.1 (min.) | ||
# Done at Tue Oct 8 14:17:27 2013 | # Done at Tue Oct 8 14:17:27 2013 | ||
===Error Counting Results=== | |||
Error Rate: 5.47% | |||
Error Rate of Insertions: 2.40% | |||
Error Rate of Deletions: 1.96% | |||
Error Rate of Substitutions: 1.11% |
Latest revision as of 00:17, 9 October 2013
HL155 Novoalign (Started 10/3/2013)[edit]
V4S1[edit]
Calmd
samtools calmd -eS novo_v4s1_sortfilt.sam V4S1_fullrevcomp.fa > novo_v4s1_sortfilteq.sam
Perl Script
perl count_mismatch.plx
Error Counting Results[edit]
Error Rate: 5.42% Error Rate of Insertions: 2.22% Error Rate of Deletions: 2.15% Error Rate of Substitutions: 1.05%
V4S2[edit]
Pipeline[edit]
Build Index
novoindex index_v4s2fullrevcomp.ndx V4S2_fullrevcomp.fa
Novoalign
novoalign -d index_v4s2fullrevcomp.ndx -f ../../s_3_1_Indx12.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s2.sam
Convert to Bam and Sort
samtools view -bS novo_v4s2.sam | samtools sort - novo_v4s2_sort
Filter
samtools view -h -F 4 -q 70 novo_v4s2_sort.bam > novo_v4s2_sortfilt.sam
Calmd
samtools calmd -eS novo_v4s2_sortfilt.sam V4S2_fullrevcomp.fa > novo_v4s2_sortfilteq.sam
Perl Error Counting Script
perl count_mismatch.plx
Alignment Results[edit]
# Read Sequences: 17308686 # Aligned: 3672898 # Unique Alignment: 3663803 # Gapped Alignment: 2517060 # Quality Filter: 44201 # Homopolymer Filter: 11 # Elapsed Time: 14209.542 (sec.) # CPU Time: 179.1 (min.) # Done at Tue Oct 8 14:17:27 2013
Error Counting Results[edit]
Error Rate: 5.47% Error Rate of Insertions: 2.40% Error Rate of Deletions: 1.96% Error Rate of Substitutions: 1.11%