ALIGNED BASES in picard

asling

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Join Date: Jun 2011

Posts: 14
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ALIGNED BASES in picard

09-14-2011, 08:25 AM

we have a bam file generated by tophat in out RNA-seq analysis, and CollectAlignmentSummaryMetrics in picard was used to evaluate the mapping quality. Our reads are pair-end, the result shows that total PF_READS_ALIGNED is 14546338, about 80% reads are mapped to the reference,which is within our expectation. However,PF_ALIGNED_BASES is only 46423220 in total, it seems too few because picard suggest that PF_ALIGNED_BASES=PF_ALIGNED_READS * READ_LENGTH,and our read_length is 85.

Do anyone have any idear about that? In picard's manul, it suggest PF_ALIGNED_BASES will be differ when many reads are aligned with gaps,but i don't quite understand about that because we didn't find anything abnormal in bam files. Our reference's coverage is 2.5X,maybe N in reference sequence is the reason?

Thanks for help
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