Get A-site Offsets

This option is preferable for spanner genomes (e.g. E. coli, S. cerevisiae) with simple gene structures and fewer introns and isoforms.
This option is preferable for complex genomes like mouse and human. The alignment file contains reads directly aligned to gene transcripts.

For genome, the annotation file could be a .tab file with the following fields (header is not needed in the .tab file):

Gene name Chromosome Strand CDS Length Number of CDS regions CDS Start 1 CDS End 1 CDS Start 2 CDS End 2
YAL008W chrI + 597 1 136914 137510
YBL087C chrII - 414 2 59822 60193 60698 60739

Alternatively, a GFF file can also be given as input for annotations, but the script is optimized for processing GFF files for E. coli and S. cerevisiae only.

Select the fasta file containing the genome sequence.

min nt, max nt

The size of the read obtained in the Ribo-Seq Next-Generation Sequencing (NGS) experiment that represents a copy of the mRNA fragment protected by the ribosome and cleaved by the RNase enzyme.

5' or 3' end
nt

Number of nucleotides beyond the CDS region of a gene which are to be avoided to overlap with another gene.

Minimum average number of reads per codon for filtering genes

Minimum percentage of genes with the most probable offset for assigning a unique offset %

Minimum ratio between the average reads in the second, third and fourth codon and the reads in the first codon

The filter file consists of a list of genes to be included or excluded in the analysis. In the file, the genes should be deliminated by tab.

Yes No

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