vRNA

There are 4 ways you can provide reads for sRNAbench to profile:

• Upload a file (typically fastq or fastq.gz)
• Provide a link/URL with your data (it will be downloaded and then profiled)
• Provide an accession for a SRA run (they start with SRR,ERR or DRR e.g. SRR1563062)
• Provide an ID from a previous sRNAbench Job to reuse an uploaded file (e.g. ZAPFTBMPBGCPIDM)

Different types of input can be provided: fastq, sra, read/count and fasta format.
The files can be provided as plain text (fastq, read/count and fasta) or compressed with gzip (*.gz extension). Please try whenever possible upload *.gz files.
Please note that sRNAbench infers the file format by means of the extension. unknown extensions are treated as read/count format. For example sample.gz would be treated as read/count format file. The program will fail if the file format is incorrectly inferred.
The recognized extensions are:
fasta: fa, fasta, fa.gz, fasta.gz
read/count: rc, rc.gz
sra: sra
fastq: fastq.gz, fastq, fq, fq.gz, FASTQ, FASTQ.gz, fastQ, fastQ.gz

File format explanation:
read/count
read/count format is tab separated with two columns: the read sequence separated by the read count (number of times this read was sequenced)
read read count
ATTACG… 3000
GCATT… 2500

fasta format:
>readID#3000
ATTACG…
>readID#2500

Note that spaces between the readID and the read count are also allowed.

You can find more info on how they were predicted on sRNAbench original paper and full manual .

Abbreviations:

• seqName:
• totalRC: total Read Count assigned to that prediction
• 5p: stands for 5'arm
• 3p: stands for 3'arm
• RC: stands for Read Count
• 5pname: name assigned to the 5' arm
• 5pseq: sequence assigned to the 5' arm
• 5pRC: Read Count assigned to the 5' arm
• align: alignment visualisation of the predicted miRNA