Standard Deviation in Fastq

Question

[savscosta]

Hi people,

I'm trying to find a method or a software to find the standard deviation of my fastq file reads.

I found this topic ( Question: Mean and SD read length from a range of fastq files ), but when i try to run the command to a small test file, I did not get the expected result when I performed the calculations manually.

Thanks

[WouterDeCoster]

the standard deviation of the reads of a file in fastq.

What does that mean?

[h.mon]

How did you manually calculated read length standard deviation? How do your results differ from the script linked? Please provide this info, and also provide a small fastq example.

[savscosta]

In this analysis I used a fastq file with three readings.

@7SALQ:01332:11604
CAAAT
+
:::09
@7SALQ:01332:11605
ACAGTAG
+
767;;;;
@7SALQ:01332:11609
TTG
+
-*-

And I manually calculated the average (which coincided with the data given by the script) and the standard deviation that did not match.

[finswimmer]

Hello,

if I see it correctly than Pierre Lindenbaum misses a sqrt in his awk solution posted in the thread you've linked. Does this give you the right answer?

$ awk 'BEGIN { t=0.0;sq=0.0; n=0;} ;NR%4==2 {n++;L=length($0);t+=L;sq+=L*L;}END{m=t/n;printf("total %d avg=%f stddev=%f\n",n,m,sqrt(sq/n-m*m));}'  *.fastq

fin swimmer