Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper

annotate README.rst @ 5:423ad61697c4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero). readingFrame function fails with subscript out of bounds. Bugfix 2: [triplet] Check if transcript name in SAM matches the name in FASTA. Produce an error message if it's not. This fixes the problem where an empty plot is produced (no bars). [ribosome_profile] - A proper error message is now produced if an invalid transcript name is provided. Updated test data
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 27 Oct 2015 12:21:50 +0000
parents c34c364ce75d
children 5a242f289347
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
1 README
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
2 ------
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
3
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
4 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
5 integration for `Galaxy <http://galaxyproject.org/>`_ /
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
6 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
7
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
8 Included tools
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
9 ..............
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
10 In the order in which they are run
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
11
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
12 #. Prepare riboSeqR Input
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
13
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
14 Prepare riboSeqR format input files from alignment files (SAM format,
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
15 Ribo-Seq or RNA-Seq alignments).
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
16
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
17 #. Triplet Periodicity
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
18
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
19 Plot triplet periodicity for different read lengths.
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
20
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
21 #. Metagene Analysis
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
22
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
23 Metagene analysis.
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
24
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
25 #. Plot Ribosome Profile
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
26
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
27 Plot Ribosome profile and output Ribo/RNA counts.
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
28
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
29 [OR]
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
30
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
31 Differential Translation Analysis
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
32
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
33 Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
34 translation analysis with baySeq.
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
35
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
36 Tested with
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
37 ...........
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
38 **R** ``3.1.2``
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
39
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
40 **riboSeqR** ``1.0.5``
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
41
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
42 **baySeq** ``2.0.50``
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
43
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
44 **rpy2** ``2.3.10``