sickle output explanation?

Question

[Azhar]

Hi I used sickle to trimme the pair end sequence in fastqc format so i used this command

sickle pe -f /pathtofile/inputfile1.fq -r /pathtofile/inputfile.fq2 -o /pathtofile/outputfile1 -p /pathtofile/outputfile2
-t sanger

and the result is like this

Total input FastQ records: 11638204 (5819102 pairs)

FastQ paired records kept: 11638204 (5819102 pairs)
FastQ single records kept: 0 (from PE1: 0, from PE2: 0)
FastQ paired records discarded: 0 (0 pairs)
FastQ single records discarded: 0 (from PE1: 0, from PE2: 0)

i think no trimming is done to make sure i check fastqc report for output files no difference was found any answers please

Answer 1

[Istvan Albert]

The proper way to think about it is to first look at the FASTQ report and determine if you need to apply trimming at all.

It is possible that quality trimming would not alter the data much - in which case quality trimming is counterproductive as any data altering step may by itself introduce additional, small biases.

Only apply the QC process if you have reason to do so - then verify the results. If there is no change it might just be that you have not applied the tool correctly, the tool does not quite operate in the way you think it does, or that your data has properties that the tool cannot deal with.

[Azhar]

Thanks Istvan Albert I understand that you said above i know offcourse we have to determine from fastqc report for trimming but my question is run the above mentioned command and there nothing happened for long time and then ihave to cntrl c .

So my question is i dont know is it worked or not ? but there was no output