Thank you very much, so what are the unpaired fastq files used for ?
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roonymoonlight •
Trimmomatic output files
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 ?
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GenoMax
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roonymoonlight •
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roonymoonlight •
1 answer
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.
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Steven Lakin
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.
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Brian Bushnell
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