Trimmomatic output files

Question

[roonymoonlight]

Hi, I have used Trimmomatic to validate my fastq files, but i have got for outputs , so i wondering which one of them i should use in Tophat or for my RNA analysis ?

Answer 1

[Steven Lakin]

Trimmomatic produces four files:

• Paired forward fastq file
• Unpaired forward fastq file
• Paired reverse fastq file
• Unpaired reverse fastq file

You want to use the paired forward and reverse fastq files as downstream input in your pipeline.

[roonymoonlight]

Thank you very much, so what are the unpaired fastq files used for ?

[Brian Bushnell]

Additional coverage, if you need it. With RNA-seq it may cause bias to remove short-insert reads (since they are more likely to come from short transcripts), which Trimmomatic outputs as unpaired when using the default settings, I believe.