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2 hours ago by

Hello there, I have aligned the sequenced reads with Bowtie aligner. After that I converted SAM output to BAM but when I checked the number of reads that were in BAM file I found a huge discrepancy in number of reads in SAM and BAM file. Is it normal to have reduced number of reads in BAM due to compression?

saddams-MBP:alfred saddamhusain$ wc MCM7_input2.sam
 41296062 558393216 7870675429 MCM7_input2.sam

saddams-MBP:alfred saddamhusain$ samtools view -Sbq 20 MCM7_input2.sam > MCM7_input2.bam
saddams-MBP:alfred saddamhusain$ wc MCM7_input2.bam
 6645739 49529627 1542136565 MCM7_input2.bam

saddams-MBP:alfred saddamhusain$ samtools view -Sb MCM7_input2.sam > MCM7_input2_without_q.bam
saddams-MBP:alfred saddamhusain$ wc MCM7_input2_without_q.bam
 7597383 57680530 1925767048 MCM7_input2_without_q.bam



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