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:
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.