RiboCount¶

Output read counts for all transcripts in an alignment.

Parameters¶

1. Ribo-Seq alignment file (Sorted BAM file)¶

A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM file should be sorted. This can be done using one of the following methods.

RiboGalaxy -> Sort Data -> Sort BAM dataset.
samtools sort input.bam inputsorted

2. Transcriptome (FASTA)¶

A FASTA format file with sequences of the transcripts.

3. Read lengths to consider [optional] (Integer - 0 or greater)¶

If this option is provided, only Ribo-Seq data of the given read length is considered. Multiple read lengths can be provided and should be separated by commas. If multiple read lengths are input, corresponding read offsets should also be specified. If you do not wish to apply an offset, please input 0 for the corresponding offset.

4. Read offset(s) corresponding to read lengths [optional] (Integer - 0 or greater)¶

If this option is provided, this offset is added to the read alignment positions. Multiple offsets should be separated by commas.

5. Restrict read counts¶

Choose whether to output read counts for the entire transcript or restrict read counts to the 5’ or 3’ region of the longest ORF. Default start (ATG) and stop codons (‘TAG’, ‘TGA’, ‘TAA’) are used to identify the longest ORF in 3 frames.

Output¶

Read counts for all transcripts in the alignment (ZIP)¶

The output file ribocount_output.zip should first be uncompressed. This will generate a folder called ribocount_output. Open index.html in a web browser to view the results of ribocount.

Total reads for each transcript will be displayed in a table along with the name of the transcript and a link to the CSV file containing the read counts in 3 frames for each position in the transcript. If 5’ or 3’ counts are requested, an extra column will be present with reads in these regions.

Command line¶

ribocount can also be run on the command line. The usage is

ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l READ_LENGTHS]
             [-s READ_OFFSETS] [-v | -r] [-m HTML_FILE]
             [-o OUTPUT_PATH] [-d]

Output read counts for all transcripts

required arguments:

`-b RIBO_FILE, --ribo_file RIBO_FILE`
	Ribo-Seq alignment file in BAM format
`-f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA`
	FASTA format file of the transcriptome

optional arguments:

`-h, --help`	show this help message and exit
`-l READ_LENGTHS, --read_lengths READ_LENGTHS`
	Read lengths to consider (default: 0). Multiple read lengths should be separated by commas. If multiple read lengths are specified, corresponding read offsets should also be specified. If you do not wish to apply an offset, please input 0 for the corresponding read length
`-s READ_OFFSETS, --read_offsets READ_OFFSETS`
	Read offsets (default: 0). Multiple read offsets should be separated by commas
`-l INTEGER, --read_length INTEGER`
	Read length to consider (default: None)
`-s INTEGER, --read_offset INTEGER`
	Read offset (default: 0)
`-v, --count_five`
	Flag. Output reads in 5’ region
`-r, --count_three`
	Flag. Output reads in 3’ region
`-m HTML_FILE, --html_file HTML_FILE`
	Output file for results (HTML)
`-o OUTPUT_PATH, --output_path OUTPUT_PATH`
	Files are saved in this directory
`-d, --debug`	Flag. Produce debug output