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.
|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.