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Old 01-10-2014, 11:07 AM   #1
arcolombo698
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Location: Los Angeles

Join Date: Nov 2013
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Default Understanding Trimmomatic Output

Hello.

So for a specific trimmomatic run, I have the following output and I wish to compare this information with FastQC

Input Read Pairs: 39100817 Both Surviving: 15397090 (39.38%) Forward Only Surviving: 12799520 (32.73%) Reverse Only Surviving: 548505 (1.40%) Dropped: 10355702 (26.48%)


where my FastQC report shows that my total input reads is
39100817, and after trimming the QC report shows 15397090

So if I take the difference between these I get 23703727

however this does not match the Dropped 10355702 from trimmomatic.

So what is this Dropped output mean?
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Old 01-10-2014, 12:21 PM   #2
usad
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Hi Acrolombo

Trimmomatic will (in this paired case) generated four files from your set of two files (FW & RV)
First a new pair of FW and RV reads which are still paired. This is indicated by "both surviving" and this is the same numer you got out of FastQC.
In addition to this paired sequences, some of your reads in FW did survive the trimming but their partner sequences didn't, these end up in a different file. Complementary some of the RV reads might survive, but their cognate FW read might have been trimmed down completely. This is the last file RV only.
As most often RV reads have lower Quality you get more reads where the FW read survived than the RV read than vice versa.

You might ask why: The issue is that if you were to drop some FW reads completely but kept their RV reads your FW.fastq file would contain a different number of reads than the RV.fastq file. As their is still useful information in unpaired reads for many aplications these are being moved to separate files.

Cheers
björn
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