Transcriptome Toolset » exRNA Tools

The pipeline generates a variety of results and intermediate files. All of these are
compressed into a single archive and uploaded to your output database.

Here is a description of the various output files:

• Read length distribution - File with extension .clipped.readLengths.txt
• .stats - Summary statistics of read counts mapped to various libraries
• short_reads.txt - reads that are too small to be considered (<15nt by default)
• reads_orig.fa - adapter clipped, collapsed reads that are within the required length
• reads.fa & readsNG.fa - these seem to be intermediate files, I do not ever use these
• reads_withAdapter.fa - should always be empty as adapters are removed
• genome.parsed - the result of the read mapping to the host genome
• reads.annotation - these are all the reads mapped to the host genome in terms of their corresponding smallRNA annotation
• hairpin/ subdirectory - read alignments against the hairpin sequences

You can find more information on other output files generated by sRNABench in this tutorial.