Albero (Tree):
e161958bab
11.0
12.0
12.1
12.2
13.0
13.1
13.37
14.0
14.1
14.2
15.0
bedlam
bedlam-name-fixes
dive
erik
gitignore
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master
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python-renames
rworkman
urchlay
user/aclemons/updates
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user/anddt/network/strongswan
user/anddt/network/umurmur
user/anddt/network/yt-dlp
user/anddt/network/znc
user/anddt/office/gnumeric
user/anddt/office/sigil
user/anddt/system/FontAwesome
user/anddt/system/conky
user/anddt/system/fakeroot
user/anddt/system/hplip-plugin
user/anddt/system/postgresql
user/anddt/system/testdisk
user/anddt/system/worker
user/anddt/system/xen
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user/chris.willing/updates
user/dslackw/updates
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willysr
wxWidgets-wip
GPG-KEY
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Dave Woodfall
8a5bd3f1e3
academic/pyCRAC: Update MD5SUM.
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2 anni fa | |
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| .. | ||
| README | 4dedcbf305 academic/pyCRAC: Updated for version 1.5.0. | 3 anni fa |
| README.tests | 4dedcbf305 academic/pyCRAC: Updated for version 1.5.0. | 3 anni fa |
| pyCRAC.SlackBuild | 586de8ca7f academic/pyCRAC: Updated for version 1.5.1. | 3 anni fa |
| pyCRAC.info | 8a5bd3f1e3 academic/pyCRAC: Update MD5SUM. | 2 anni fa |
| setup_slack.py | 586de8ca7f academic/pyCRAC: Updated for version 1.5.1. | 3 anni fa |
| slack-desc | 15fbb17347 academic/pyCRAC: Added (Next generation sequencing analysis). | 7 anni fa |
| test_slack.sh | 2f3ac418ad academic/pyCRAC: Updated for version 1.4.4. | 5 anni fa |
README
The pyCRAC package is a collection of python scripts to analyse high
throughput data generated by RNA-sequencing, especially of molecules
crosslinked by UV to an immunoprecipitated protein of interest (i.e.
data generated by CLIP or CRAC protocols).
It can be used to remove duplicate reads,tackles directional libraries
and reports sense and anti-sense hits.
Included is the pipeline used for the analysis of a group of CRAC data
sets.
References
Genome Biol. 2014 Jan 7;15(1):R8. doi: 10.1186/gb-2014-15-1-r8.
PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription
termination regulates expression of hundreds of protein coding genes in
yeast. Webb S, Hector RD, Kudla G, Granneman S.
Nature Communications, 2017; DOI: 10.1038/s41467-017-00025-5
Kinetic CRAC uncovers a role for Nab3 in determining gene expression
profiles during stress. van Nues R, Schweikert G, de Leau E, Selega
A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G,
Granneman S.
If you want to run the test suite after installation, see README.tests.
Note on the Crac pipelines:
Use the -h flag to get a detailed help menu.
The CRAC_pipeline_PE.py script needs to be run from the folder that
contains the fastq files
The barcode list file should contain two tab-separated columns in which
the first column is the barcode sequence and the second column is the
name of the experiment
The file containing the adapter sequences should be in the fasta format.
The chromosome_lengths file should contain two tab-separated columns in
which the first column has the chromosome name and the second the
chromosome length.
throughput data generated by RNA-sequencing, especially of molecules
crosslinked by UV to an immunoprecipitated protein of interest (i.e.
data generated by CLIP or CRAC protocols).
It can be used to remove duplicate reads,tackles directional libraries
and reports sense and anti-sense hits.
Included is the pipeline used for the analysis of a group of CRAC data
sets.
References
Genome Biol. 2014 Jan 7;15(1):R8. doi: 10.1186/gb-2014-15-1-r8.
PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription
termination regulates expression of hundreds of protein coding genes in
yeast. Webb S, Hector RD, Kudla G, Granneman S.
Nature Communications, 2017; DOI: 10.1038/s41467-017-00025-5
Kinetic CRAC uncovers a role for Nab3 in determining gene expression
profiles during stress. van Nues R, Schweikert G, de Leau E, Selega
A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G,
Granneman S.
If you want to run the test suite after installation, see README.tests.
Note on the Crac pipelines:
Use the -h flag to get a detailed help menu.
The CRAC_pipeline_PE.py script needs to be run from the folder that
contains the fastq files
The barcode list file should contain two tab-separated columns in which
the first column is the barcode sequence and the second column is the
name of the experiment
The file containing the adapter sequences should be in the fasta format.
The chromosome_lengths file should contain two tab-separated columns in
which the first column has the chromosome name and the second the
chromosome length.