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Add help section in xml and update usage documentation
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Mon, 17 Aug 2015 10:27:58 +0100
parents 096c6bbf4a04
children 8964641b04ef
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6 -------- 6 --------
7 Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM). 7 Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM).
8 8
9 Parameters 9 Parameters
10 .......... 10 ..........
11 1. Ribo-Seq alignment file (sorted BAM) 11 1. Ribo-Seq alignment file (Sorted BAM file)
12 A bowtie 1 12
13 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
14 file should be sorted. This can be done using one of the following methods.
15
16 1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
17 2. ``samtools sort input.bam inputsorted``
18
19 2. Transcriptome (FASTA)
20
21 A FASTA format file with sequences of the transcripts.
22
23 3. Name of the transcript to plot (Text)
24
25 The name of the transcript to plot **should** match the name in the transcriptome (FASTA)
26 and the Ribo-Seq/RNA-Seq alignment (BAM).
27
28 4. RNA coverage [optional] (Sorted BAM file)
29
30 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
31
32 5. Read lengths to consider [Optional] (Integer - 0 or greater)
33
34 If this option is provided, only Ribo-Seq data of the given length is considered.
35
36 6. Offset [optional] (Integer - 0 or greater)
37
38 If this option is provided, this offset is added to the read alignment positions.
39
40 Output
41 ......
42 1. Plots (PNG and SVG)
43
44 Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue)
45
46 RNA coverage as a gray background (if the RNA coverage option was selected).
47
48 The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames.
49
50 The color codes are start (white) and stop (dark gray).
51
52 .. image:: ../images/riboplot.png
53
54 2. RiboSeq read counts in 3 frames for each position in the transcript (CSV)
55
56
57 Command line
58 ............
59 ``riboplot`` can also be run on the command line. The usage is ::
60
61 usage: python riboplot.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT
62 [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE]
63 [-o OUTPUT_PATH] [-d]
64
65 Plot and output read counts for a single transcript
66
67 optional arguments:
68 -h, --help
69 show this help message and exit
70
71 -n RNA_FILE, --rna_file RNA_FILE
72 RNA-Seq alignment file (BAM)
73
74 -l INTEGER, --read_length INTEGER
75 Read length to consider (default: None)
76
77 -s INTEGER, --read_offset INTEGER
78 Read offset (default: 0)
79
80 -m HTML_FILE, --html_file HTML_FILE
81 Output file for results (HTML)
82
83 -o OUTPUT_PATH, --output_path OUTPUT_PATH
84 Files are saved in this directory
85
86 -d, --debug
87 Flag. Produce debug output
88
89 required arguments:
90 -b RIBO_FILE, --ribo_file RIBO_FILE
91 Ribo-Seq alignment file in BAM format
92
93 -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
94 FASTA format file of the transcriptome
95
96 -t TEXT, --transcript_name TEXT
97 Transcript name
13 98
14 RiboCount 99 RiboCount
15 --------- 100 ---------
101 Output read counts for all transcripts in an alignment.
16 102
103 Parameters
104 ..........
105 1. Ribo-Seq alignment file (Sorted BAM file)
106
107 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
108 file should be sorted. This can be done using one of the following methods.
109
110 1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
111 2. ``samtools sort input.bam inputsorted``
112
113 2. Transcriptome (FASTA)
114
115 A FASTA format file with sequences of the transcripts.
116
117 3. Read lengths to consider [optional] (Integer - 0 or greater)
118
119 If this option is provided, only Ribo-Seq data of the given length is considered.
120
121 4. Offset [optional] (Integer - 0 or greater)
122
123 If this option is provided, this offset is added to the read alignment positions.
124
125 Output
126 ......
127 Read counts for all transcripts in the alignment (ZIP)
128
129 The output file ``ribocount_output.zip`` should first be uncompressed. This will generate
130 a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount.
131
132 Total reads for each transcript will be displayed in a table along with the name of the transcript and a link
133 to the CSV file containing the read counts in 3 frames for each position in the transcript.
134
135 .. image:: ../images/ribocount.png
136
137 Command line
138 ............
139 ``ribocount`` can also be run on the command line. The usage is ::
140
141 usage: python ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER]
142 [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d]
143
144 Output read counts for all transcripts
145
146 optional arguments:
147
148 -h, --help show this help message and exit
149
150 -l INTEGER, --read_length INTEGER
151 Read length to consider (default: None)
152
153 -s INTEGER, --read_offset INTEGER
154 Read offset (default: 0)
155
156 -m HTML_FILE, --html_file HTML_FILE
157
158 Output file for results (HTML)
159
160 -o OUTPUT_PATH, --output_path OUTPUT_PATH
161 Files are saved in this directory
162
163 -d, --debug Flag. Produce debug output
164
165 required arguments:
166
167 -b RIBO_FILE, --ribo_file RIBO_FILE
168 Ribo-Seq alignment file in BAM format
169
170 -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
171 FASTA format file of the transcriptome
172