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Alleyoop (version 0.4.3+galaxy1)
Select a built-in FASTA file (if available) or one from the history
Select genome from the list
Minimum base quality for T>C conversions (default: 27).
Maximum read length (before trimming).
If this option is set to Yes, the Alleyoop read-separator module will be run to output BAM files of separated T>C reads from non T>C reads. Default: No


SLAMseq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability.

Original publication: Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435


Alleyoop (Additional sLamdunk heLpEr tools for anY diagnOstics Or Plots) is a collection of tools for post-processing and running diagnostics on Slamdunk analyses. This tool works on the output of the Slamdunk tool and requires all the inputs listed in the table below.

Parameter Description
Genome The reference fasta file (Genome assembly).
Reference BED-file containing coordinates for 3' UTRs.
Reads Slamdunk Filtered BAM files.
Counts Slamdunk Count TSV files.
Variants Slandunk VCF files.
Read length Maximum length of reads (usually 50, 100, 150).

This tool runs the Alleyoop summary, rates, utrrates, tcperreadpos and tcperutrpos modules and outputs:

  • Tab-separated summary files from the summary module with mapping and PCA statistics
  • Tab-separated stats files from the rates, utrrates, tcperreadpos and tcperutrpos modules

Optionally, the read-separator module can be run to output BAM files of separated T>C and non T>C reads.

The summary and stats files can be summarised and visualised with MultiQC. An example MultiQC report can be seen here. For information on these modules see the Alleyoop documentation.