Hi All
Trying to use bbmap to align some Illumina PE reads. My command line looks like this
When I do this out.sam contains alignments of only read1 though the log indicates that read2 reads were aligned
If I change the command line to
Read2 reads are indeed aligned.
Any thoughts what I'm doing wrong not to get paired end alignments with the first command line? I am using BBMap version 35.92.
Thanks
Mark
Trying to use bbmap to align some Illumina PE reads. My command line looks like this
Code:
bbmap.sh overwrite=t ref=A.fasta in=R1_001_val_1.100.fq in2=R2_001_val_2.100.fq minid=0.25 mappedonly=true out=out.sam outu=unaligned_reads.fa maxindel=100000
Code:
Read 1 data: pct reads num reads pct bases num bases mapped: 100.0000% 100 100.0000% 29779 unambiguous: 100.0000% 100 100.0000% 29779 ambiguous: 0.0000% 0 0.0000% 0 low-Q discards: 0.0000% 0 0.0000% 0 perfect best site: 0.0000% 0 0.0000% 0 semiperfect site: 35.0000% 35 35.1758% 10475 rescued: 0.0000% 0 Match Rate: NA NA 88.8176% 26449 Error Rate: 65.0000% 65 4.4763% 1333 Sub Rate: 65.0000% 65 0.3627% 108 Del Rate: 0.0000% 0 0.0000% 0 Ins Rate: 49.0000% 49 4.1136% 1225 N Rate: 100.0000% 100 6.7061% 1997 Read 2 data: pct reads num reads pct bases num bases mapped: 100.0000% 100 100.0000% 25636 unambiguous: 100.0000% 100 100.0000% 25636 ambiguous: 0.0000% 0 0.0000% 0 low-Q discards: 0.0000% 0 0.0000% 0 perfect best site: 0.0000% 0 0.0000% 0 semiperfect site: 26.0000% 26 25.3745% 6505 rescued: 2.0000% 2 Match Rate: NA NA 86.8232% 22258 Error Rate: 74.0000% 74 4.9852% 1278 Sub Rate: 74.0000% 74 0.8894% 228 Del Rate: 0.0000% 0 0.0000% 0 Ins Rate: 42.0000% 42 4.0958% 1050 N Rate: 100.0000% 100 8.1916% 2100
If I change the command line to
Code:
bbmap.sh overwrite=t ref=A.fasta in=R2_001_val_2.100.fq minid=0.25 mappedonly=true out=out.sam outu=unaligned_reads.fa maxindel=100000
Any thoughts what I'm doing wrong not to get paired end alignments with the first command line? I am using BBMap version 35.92.
Thanks
Mark