DARIO requires mapped reads/tags and/or the user annoated loci stored
in the bed
format as input. Note that we only support data originating from experiments
prepared with the short RNA-seq protocol and thus predominantly covers read lengths of about 22-24nt.
The mapped reads have to be in the following format:
#chr start end id nb of sequenced reads strand
chr1 20229 20366 GSM34290_325 50 +
chr1 1092347 1092441 GSM34290_326 3 +
To avoid big file sizes, it is advised to map tags (unique set of sequences), instead of all reads.
The number of times each tag was sequenced has to be stored in the "nb of sequenced reads" field of the bed file.
If you want to upload your own annotation file or a file with some interesting locations,
you have to create a bed file (filename must have correct suffix like .bed or bed.gz) with the following columns:
#chr start end id score strand type source
chr1 20229 20366 hsa-mir-1302-2 0 + miRNA miRBase_v16
chr1 1092347 1092441 hsa-mir-200b 0 + miRNA miRBase_v16
Mapping Tools and List of Supported Reference Genomes
As a first step, the sequenced reads must be mapped to a reference
genome, using tools like:
DARIO supports the following assemblies as reference genomes:
Converting mapping results into BED file format
To convert the output of your read mapper to the bed format, you can
script. This script will not only create a bed formatted file, but
also merge mapped reads to tags and try to pack the output file. This
way, the file size will be minimized as much as possible. (Note: It might be necessary to explicitly select 'SAM
format' as output format when running your mapping tool). The SAM file must contain header information.
SAM format (output from segemehl, Bowtie, BWA, ...):
perl map2bed.pl -i mapping.sam -f 1 -o upload.bed
SOAP format (output from SOAP):
perl map2bed.pl -i mapping.soap -f 2 -o upload.bed
Example BED files
Example BED-files containing previously mapped reads can be found on this page.
Converting mapping results into BAM file format
To convert the output of your read mapper to the BAM format, you can
Assure that the output format of your mapping tool
is the SAM format and call samtools as follows:
samtools view -bS yourFile.sam > yourFile.bam
NOTICE: You have to call samtools with the -S parameter, otherwise you will loose the header information of the SAM file, which is mandatory for our calculations!