a microRNA portal in deep sequencing era
miR-target & Expression
Search keyword(s) :
or Import your own data in BAM file fomat (file size <
*Note: To avoid long upload time, we recommend using the BAM alignment file only for the miRNAs of interest.
Please use 'samtools view' to select the genomic loci for miRNAs and merge the result using 'samtools merge'.
or Upload the miR-seq browser file (*.msb) to recall any previous views saved. [
Preparing BAM file for user data
1. Make a FASTA file with unique reads only using the 'collapse_reads.pl' script in miRDeep2.
This removes duplicate reads and leaves read count in the title line as in
where 10 indicates the read count.
2. Map the unique reads to the hg19 human reference genome or premature miRNA sequences.
We recommend using 'Bowtie -a -S out.sam -v 0' for perfect matches.
'-v 0' option should be modified to allow mismatches.
3. Convert the SAM file into BAM file (
to select alignment for miRNAs of interest only.
This step is optional, but will reduce the file size and uploading time.
samtools view aln.sorted.bam chr2:20,100,000-20,200,000
samtools merge out.bam in1.bam in2.bam in3.bam
There would be some browser limitations except Chrome browser. Users can search informations with older browsers but some features may not be supported.
We recommend to use newest version of
browser for miRGator v3.0.
We welcome any suggestion to include new data sets on miRNA biology (e.g. miRNA profiles, miRNA-related mRNA profiles and so on).