tsRFun

Inputs of tsRFinder and tsRTarget section require users input collapsed FASTA data. The data are recommended to be compressed to increase the uploading speed.

Firstly, users should filter the adapters and low quality reads from raw fastq data. Trim_galore and some other software can trim the adapters and low quality reads at same time.

Then, users should collapse the clean fastq reads to fasta reads. The conversion can be done by the following code in Linux.

The collapsed fasta reads are required as input format, and the reads should be named by unique tags (e.g. “>seq_1_x1”. The name includes three parts, first part is “>seq”, the second part “1” represent the unique id, the last “x1” represent the count number of read, and “_” acts as a connector in the tag).

tRFfinder supports only inputs in FASTA format. FASTA is a plain-text format for representing DNA, RNA or protein sequences. Every nucleotide or amino acid is represented by single-letter. For details on FASTA format, please see FASTA Format in Wikipedia.

For tRFfinder, only FASTA fromat for RNA sequences is supported. There are mainly two ways to input your sequence:

It might take some time for tRFfinder to predict the tRFs. Please wait for a minute. On the "Predict Results" page, there are several important components.

tsRTarget will show the potential canonical and non-canonical tsRNA-mRNA interactions based on CLIP-Seq and CLASH data.

For CLIP-Seq data, we clustered the unique CLIP reads overlapped in genome reference, and ranked them by peak high. The observed peak height can reflect the binding affinity and RNA abundance.

For CLASH/CLEAR data, we used duplex reads mapping for ultra-short RNA strands to multi references, and allow the 1-2 mismatches because the potential contaminants during the crosslinking.

tRFinCancer provides expression landscapes of tsRNAs across mutiple types of cancer tissues. The usage is desribed below.

tsRFunciton helps users predict the functions of tsRNAs by performing GO enrichment analysis on their potential targets. The enrichment analysis will be determined by using a hypergeometric test and FDR correction.