Interpreting Stats output of SAM tools

Question: Interpreting Stats output of SAM tools

21 months ago by

Would greatly appreciate if someone can explain to me the difference between the two BAM summary numbers, namely; "raw total sequences" and "sequences" that appears on the output of the Stats module in SAMTools.

I used Stats of SAMTools to generate summary statistics for a pooled BAM file. In the output I got, "raw total sequences" = "sequences". Does it mean that all my raw sequences were usable sequences and none were filtered out?

Best Rgds, Hasitha.

bam samtools chip-seq • 2.4k views

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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by hpremathilake • 20

21 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If none were filtered, then yes, these counts will be the same.

This is an example stats report from a BAM dataset that did have some minor filtering:

# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. 
SN  raw total sequences:    48520                                                                                                                                                                   
SN  filtered sequences: 2                                                                                                                                                               
SN  sequences:  48518

Samtools help - most command line options are implemented in the Galaxy wrapped tool versions: http://www.htslib.org/doc/samtools.html

Thanks! Jen, Galaxy team

ADD COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, So the "sequences" = usable sequence is it? that can be used to map against the reference genome. Best, Hasitha.

ADD REPLY • link written 21 months ago by hpremathilake • 20

Hi Hasitha,

The sequences pass the filtering criteria you used, but that doesn't necessarily mean that they are usable/mappable. Run a tool like FastQC to check the quality and trim/filter if needed.

Assessing fastq data quality and many other common operations are explained here: https://new.galaxyproject.org/tutorials/ngs/#fastq-manipulation-and-quality-control

Take care, Jen

ADD REPLY • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks, Jen. You too. With all this adverse weather

ADD REPLY • link written 21 months ago by hpremathilake • 20

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