How to find the # of reads and # of bases being removed?

[prs321]

I am trying to test cutadapt and scythe to see which one is the better adapter cutter.

I am then using sickle, SolexaQA, and cutadapt in order to quality trim and then see which one does the best job.

After I have my processed paired end reads, I will then map the reads (NovoAlign) to the reference genome.

I will then proceed to compare all of these files to a control, which has no adapters cut and no quality trimming.

How do I find the # of reads and # of bases being removed before and after processing?

Should I keep look at the numbers after I cut adapter sequences or after I cut adapter sequences AND quality trim?

How do I know which combination had better mapping results?

[JamieHeather]

Not sure about the rest, but if you want to see how many reads/bases are being lost, just count how many you have before and after.

[prs321]

Not sure about the rest, but if you want to see how many reads/bases are being lost, just count how many you have before and after.

So do I need to just use wc -l in the command line and then divide by 4 and compare that number to the original?

[GenoMax]

So do I need to just use wc -l in the command line and then divide by 4 and compare that number to the original?

Or you could run FastQC before and after.

[prs321]

Or you could run FastQC before and after.

Ahh I see, thanks

[JamieHeather]

Thinking about it, you could just do it all in one wc command:

sed '1~4d;3~4d;4~4d' FILE.fq | wc -lm

That'll give you the number of reads (or lines, only counting every sequence line) and the number of characters in those reads.

Off the top of my head, I think that wc will count the newline characters as well, so if you deduct one character per read off the total characters you'll get the actual number.