Applications/Crop - Revision history

Pysdlb: /* Batch Script */

2022-11-17T14:25:21Z

‎Batch Script

Pysdlb: /* Module */

2022-11-17T11:40:30Z

‎Module

Pysdlb: /* Next Steps */

2022-11-16T10:39:59Z

‎Next Steps

Pysdlb: /* Navigation */

2022-11-16T10:39:51Z

‎Navigation

Pysdlb at 16:52, 8 November 2022

2022-11-08T16:52:52Z

Pysdlb at 11:19, 24 May 2019

2019-05-24T11:19:51Z

Pysdlb at 15:40, 10 April 2017

2017-04-10T15:40:53Z

Pysdlb at 15:39, 10 April 2017

2017-04-10T15:39:43Z

Pysdlb: Pysdlb moved page Crop to Applications/Crop without leaving a redirect

2017-04-10T15:32:29Z

Pysdlb moved page Crop to Applications/Crop without leaving a redirect

Pysdlb: Created page with "TOC ==Application Details== Description: Version: 1.33 (compiled with gcc-6.3.0) Module: ffmpeg/3.0.2 Licence: GNU ==Usage== CROP, which stands for "Clustering 16s..."

2017-04-10T15:24:02Z

Created page with "__TOC__ ==Application Details== *Description: *Version: 1.33 (compiled with gcc-6.3.0) *Module: ffmpeg/3.0.2 *Licence: GNU ==Usage== CROP, which stands for "Clustering 16s..."

New page

__TOC__
==Application Details==
*Description:
*Version: 1.33 (compiled with gcc-6.3.0)
*Module: ffmpeg/3.0.2
*Licence: GNU

==Usage==

CROP, which stands for "Clustering 16s rRNA for OTU Prediction", is a software developed in Ting Chen's Lab at University of Southern California in 2011 by Haoxiao Lin, Rui Jiang and Ting Chen.

CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate.

To know more about the theoretical basis of CROP, please refer to the following paper: Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering, Bioinformatics (2011)

===Module===

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[username@login01 ~]$ module add crop/1.33/gcc-6.3.0
[username@login01 ~]$ CROPLinux –i MyInput.fasta

</pre>

See https://github.com/tingchenlab/CROP/blob/master/CROP%20User's%20Guide%20v1.33.pdf for further details on options used.

==Further Information==

* [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

@@ Line 30: / Line 30: @@
 ===Batch Script===
-<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
+<pre style="font-family: monospace, sans-serif;">
 #!/bin/bash
 #SBATCH -J jobname                # Job name, you can change it to whatever you want

@@ Line 14: / Line 14: @@
 To know more about the theoretical basis of CROP, please refer to the following paper: Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering, Bioinformatics (2011)
-===Module===
+===Interactive Session===
 <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@login01 ~]$ module add crop/1.33/gcc-6.3.0
+[username@login01 ~]$ interactive
-[username@login01 ~]$ CROPLinux –i MyInput.fasta
+salloc: Granted job allocation 3619731
 </pre>
 See https://github.com/tingchenlab/CROP/blob/master/CROP%20User's%20Guide%20v1.33.pdf for further details on the options used.
 ==Next Steps==

← Older revision		Revision as of 10:39, 16 November 2022
Line 29:		Line 29:

	* [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP]		* [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP]
−

	{{Modulepagenav}}		{{Modulepagenav}}

← Older revision		Revision as of 10:39, 16 November 2022
Line 31:		Line 31:


−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 8: / Line 8: @@
 ==Usage==
-CROP, which stands for "Clustering 16s rRNA for OTU Prediction", is a software developed in Ting Chen's Lab at University of Southern California in 2011 by Haoxiao Lin, Rui Jiang and Ting Chen.
+CROP, which stands for "Clustering 16s rRNA for OTU Prediction", is a software developed in Ting Chen's Lab at the University of Southern California in 2011 by Haoxiao Lin, Rui Jiang and Ting Chen.
 CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate.
@@ Line 23: / Line 23: @@
 </pre>
-See https://github.com/tingchenlab/CROP/blob/master/CROP%20User's%20Guide%20v1.33.pdf for further details on options used.
+See https://github.com/tingchenlab/CROP/blob/master/CROP%20User's%20Guide%20v1.33.pdf for further details on the options used.
-==Further Information==
+==Next Steps==
 * [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP]

@@ Line 31: / Line 31: @@
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 3: / Line 3: @@
 *Description:
 *Version: 1.33 (compiled with gcc-6.3.0)
-*Module: ffmpeg/3.0.2
+*Module: crop/1.33/gcc-6.3.0
 *Licence: GNU

← Older revision		Revision as of 15:39, 10 April 2017
Line 29:		Line 29:

	* [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP]		* [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP]
		+

	{\|		{\|

← Older revision	Revision as of 15:32, 10 April 2017
(No difference)