How can read-count from BAM file be greater than than from fastq file?
This may be an odd question, but I recently aligned a fastq file (from mouse total-RNA seq) using STAR, and I wanted to get the total read count for further analysis. I tried to get it from the fastq file using
echo $(cat myfile.fastq|wc -l)/4|bc
And the number was 18,526,266.
I then also thought of trying to get it using the BAM file using
samtools flagstat myfile.bam
And the result was -
23712455 + 0 in total (QC-passed reads + QC-failed reads) 6132434 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 23712455 + 0 mapped (100.00% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)
I don't understand how the fastq file gives me 18,526,266 reads and the BAM file gives 23,712,455, which is much larger than the result from the former. What am I missing?
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