CLASHub 1.4 Analyzer Tutorial

CLASHub Analyzer includes CLASH V2, miRNA-seq V2, RNA-seq V2, cumulative fraction curve analysis, and job status monitoring.

For sequencing analyses, public data is the recommended starting point. Enter an accession and CLASHub will check, retrieve, and process the selected files. Uploading your own files remains available.

Analyze public data

Choose CLASH V2, miRNA-seq V2, or RNA-seq V2.
Select Public data and enter a run or study accession.
Select the runs you want to analyze and verify the detected species.
Enter your email and confirm the request.
Use the Job ID from the confirmation message to follow progress and open the results.

Before analysis, CLASHub checks archive metadata, read layout, species, file size, and checksums. Public files are transferred directly to CLASHub; users do not need to download and upload them.

CLASH V2 analysis

Enter one GSE, PRJNA, or SRP study, or up to 20 SRR runs. CLASH V2 supports AGO CLASH and compatible AGO-CLIP data for Human, Mouse, Drosophila, and C. elegans.

The results distinguish read-supported Direct interactions, AGO peak-supported candidate sites, and exact sites supported by both evidence types. Outputs include an HTML report, a miRNA-target result table, and an AGO coverage track when available.

miRNA-seq V2 analysis

Enter one GSE, PRJNA, or SRP study, or up to 12 SRR runs. Runs remain separate samples in the resulting matrix.

Outputs include raw miRNA counts, CPM values, isomiR information, preprocessing records, and an HTML report.

RNA-seq V2 analysis

Enter one GSE, PRJNA, or SRP study, one supported Dryad dataset, or up to 20 SRR runs. Select the samples and library settings before confirmation.

RNA-seq V2 produces gene counts and TPM values for each sample. Optional exon and intron count matrices can also be requested. Group comparison and differential expression are not part of the current V2 quantification form.

Upload files

Select Upload files if the data is not available from a supported public repository. The sequencing tools accept their listed paired-end or single-end FASTQ.gz inputs; CLASH V2 and miRNA-seq V2 also support cleaned FASTA.gz inputs.

Automatic adapter and read-structure detection is the default for FASTQ data. Public protocol information may be reviewed with AI assistance, but the executed adapter and UMI plan is selected only after deterministic read-evidence and remapping safety checks. FASTQ sequences and read names are not sent to the AI reviewer.

Cumulative fraction curve analysis

Upload a differential gene-expression CSV, select the species and miRNA, choose the analysis options, and submit the request. The output includes cumulative fraction curve graphics and a merged target-classification table.

Job status

Enter a Job ID to check whether an analysis is waiting, running, completed, or failed. Completed jobs provide links to the available reports and data files.

Analyzer results remain private job files and are not automatically added to the public CLASHub Database.