Aligned read loss after SAM to BAM conversion?

Question

[saddamhusain77]

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

Answer 1

[swbarnes2]

Don't measure bam files with wc. They are compressed. Use samtools flagstat.

Posting that username on a public board is certainly a ...choice.

[saddamhusain77]

Thanks @swbarnes2, I get it. I am sorry but I don't get what you mean by "Posting that username on a public board is certainly a ...choice"

[Ram]

Is your real name Saddam Husain? If not, you might better off choosing a different username as Saddam Hussein of Iraq is a pretty controversial person.

[saddamhusain77]

@RamRS, not exactly as last name contains double 'S'. I hope it wouldn't have affected Biostars name policy if there is one, nor my ability to put or being answered to a question.

[Ram]

Don't worry about it - it's not a big deal.