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[GiantSpaceRobot]

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[ugoiannacchero]

Hi Paul,

I'm very new to this type of analysis, and I'm interested in tRFs. I wanted to ask whether your tool can handle only single-end sequencing data or if it supports specific formats of paired-end data, such as interleaved paired ends.

It would be helpful to know because I attempted to provide the fastq files containing both mate1 and mate2 as input, but I received two different outputs. Since the files that I need to analyze are Paired Ends and they come from a sequencing reads archive (SRA), is it possible that your tool requires the fastq-dump data to remain unsplit?

Thank you in advance!