Dear all,
Seems I'm missing something trivial, but cant figure out.
I've got exome seq pipeline. 2 fastq files with corresponding paired reads. Both fastq files contain 92110130 reads each. I am aligning to hg19 as follows:
bwa mem hg19.fa -t 8 -I R1_001.fastq.gz R2_001.fastq.gz > alignment.sam
Then converting to BAM:
samtools view -bS alignment.sam > alignment.bam
Then checking the statistics:
samtools flagstat alignment.bam
Output of last command is:
92171082 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
91296311 + 0 mapped (99.05%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Question: where did all pairing info go?
Seems I'm missing something trivial, but cant figure out.
I've got exome seq pipeline. 2 fastq files with corresponding paired reads. Both fastq files contain 92110130 reads each. I am aligning to hg19 as follows:
bwa mem hg19.fa -t 8 -I R1_001.fastq.gz R2_001.fastq.gz > alignment.sam
Then converting to BAM:
samtools view -bS alignment.sam > alignment.bam
Then checking the statistics:
samtools flagstat alignment.bam
Output of last command is:
92171082 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
91296311 + 0 mapped (99.05%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Question: where did all pairing info go?
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