The problem using samtools stats

Question

[934963534]

There is information of "ACGT content per cycle" What does the cycle mean?

Also I see there are lines start with GCC and has the information of the persentages of A G C T, I wonder if it is the information of the A G C T distribution of each sequence base.

Thank you for your answering!

[lakhujanivijay]

What is the command that you are running? Also, please share it's output.

Answer 1

[Devon Ryan]

The wording of "ACGT content per cycle" comes from Sanger and Illumina sequencing. A "cycle" in this context is a base, so the first cycle is the first base in all alignments, the second cycle is the second base and so on. In some experiments (namely whole genome sequencing) one expects the amount of ACGT to be constant across "cycles". In many other types of experiments (e.g., RNAseq or amplicon sequencing), this is not the case. Either way, the graph output by FastQC is probably more useful than what samtools stats is giving you.

Yes, the GCC lines have the per-cycle ACGT content, which is why they're preceded by:

# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]

[934963534]

Thanks, I have got it.