I'm aligning 150bp paired end Illumina data to a reference with bbmap
~/BioInfo/bin/BBMap_38.06/bbmap/bbmap.sh \
pairedonly=t \
ambiguous=toss \
killbadpairs=t \
pairlen=1000 \
trimq=13 \
mintrimlength=100 \
minaveragequality=15 \
outm=SMX008C05-00067_S67_L001.aligned.sam \
outu=SMX008C05-00067_S67_L001.unaligned.sam \
showprogress=10000 \
scafstats=SMX008C05-00067_S67_L001.scafstats \
in=SMX008C05-00067_S67_L001_R1_001.500.fastq.gz \
in2=SMX008C05-00067_S67_L001_R2_001.500.fastq.gz \
ref=~/BioInfo/PROJECTS/10-18/MAIZE_B73_REF_5_GENOME \
path=~/BioInfo/PROJECTS/10-18/
Looking at the log data I see
Pairing data: pct pairs num pairs pct bases num bases
mated pairs: 49.8000% 249 49.8000% 74700
bad pairs: 0.0000% 0 0.0000% 0
insert size avg: 311.07
Read 1 data: pct reads num reads pct bases num bases
mapped: 70.8000% 354 70.8000% 53100
unambiguous: 49.8000% 249 49.8000% 37350
ambiguous: 21.0000% 105 21.0000% 15750
low-Q discards: 0.4000% 2 0.4000% 300
perfect best site: 37.6000% 188 37.6000% 28200
semiperfect site: 37.8000% 189 37.8000% 28350
rescued: 1.4000% 7
Match Rate: NA NA 98.5503% 36913
Error Rate: 13.6364% 57 1.4203% 532
Sub Rate: 13.3971% 56 0.8997% 337
Del Rate: 1.4354% 6 0.2830% 106
Ins Rate: 2.3923% 10 0.2376% 89
N Rate: 0.9569% 4 0.0294% 11
Read 2 data: pct reads num reads pct bases num bases
mapped: 67.8000% 339 67.8000% 50850
unambiguous: 49.8000% 249 49.8000% 37350
ambiguous: 18.0000% 90 18.0000% 13500
low-Q discards: 3.8000% 19 3.8000% 2850
perfect best site: 31.8000% 159 31.8000% 23850
semiperfect site: 32.2000% 161 32.2000% 24150
rescued: 2.6000% 13
Match Rate: NA NA 61.7362% 36817
Error Rate: 21.8905% 88 38.2420% 22806
Sub Rate: 21.6418% 87 0.6925% 413
Del Rate: 1.2438% 5 37.3700% 22286
Ins Rate: 1.9900% 8 0.1794% 107
N Rate: 0.7463% 3 0.0218% 13
This seems to indicate both read1 and read2 were aligned. But when I look at the output of aligned reads (SMX008C05-00067_S67_L001.aligned.sam
) it contains only read1 alignments.
Any thoughts?
Thanks
How are you looking at the alignments? Could you post the output of:
Also
Note I also tried stripping out all parameters other than ones directly related to input or file output and likewise only see read1 alignments