Applications/Bowtie1 - Revision history

Pysdlb: /* Batch Job */

2022-11-17T10:45:13Z

‎Batch Job

Pysdlb: /* Usage Examples */

2022-11-17T09:58:52Z

‎Usage Examples

Pysdlb: /* Navigation */

2022-11-16T10:38:25Z

‎Navigation

Pysdlb at 11:14, 24 May 2019

2019-05-24T11:14:49Z

Pysdlb at 14:07, 7 June 2018

2018-06-07T14:07:00Z

Pysdlb at 08:38, 6 April 2017

2017-04-06T08:38:59Z

Pysdlb: Pysdlb moved page Bowtie1 to Applications/Bowtie1 without leaving a redirect

2017-04-06T08:16:45Z

Pysdlb moved page Bowtie1 to Applications/Bowtie1 without leaving a redirect

Pysdlb at 08:16, 6 April 2017

2017-04-06T08:16:07Z

Pysdlb: Created page with "==Application Details== * Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of ove..."

2017-04-06T08:13:05Z

Created page with "==Application Details== * Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of ove..."

New page

==Application Details==

* Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
* Version: 1.1.2
* Modules: bowtie1/1.1.2
* Licence: Open source (Github)

==Usage Examples==

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small

It provides the following tools:

* bowtie
* bowtie-align-l
* bowtie-align-l-debug
* bowtie-align-s
* bowtie-align-s-debug
* bowtie-build
* bowtie-buildc
* bowtie-build-l
* bowtie-build-l-debug
* bowtie-build-s
* bowtie-build-s-debug
* bowtie-inspect
* bowtie-inspect-l
* bowtie-inspect-l-debug
* bowtie-inspect-s
* bowtie-inspect-s-debug

With linkages to the following modules too:

* [[applications/Cufflinks|Cufflinks]]
* [[applications/Samtools|Samtools]]
* [[applications/Tophat|Tophat]]
* [[applications/Samtools|Samtools]]
* [[aaplications/Bowtie2|Bowtie2]]

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

[username@login01 ~]$ module load cufflinks/2.2.1

</pre>

==Further Information==

* [http://bowtie-bio.sourceforge.net/tutorial.shtml http://bowtie-bio.sourceforge.net/tutorial.shtml]

{|
|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 57: / Line 57: @@
 #SBATCH -t 1:00:00
 #SBATCH -p=compute
 module load bowtie1/1.1.21 samtools/gcc/1.3.1

← Older revision		Revision as of 09:58, 17 November 2022
Line 46:		Line 46:
	[username@login01 ~]$ module add bowtie1/1.1.21		[username@login01 ~]$ module add bowtie1/1.1.21

		+	</pre>
		+
		+	===Batch Job===
		+	<!-- example from: https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/sequence-alignment-bowtie -->
		+	<pre>
		+	#!/bin/bash
		+
		+	#SBATCH -J bowtie_testing
		+	#SBATCH -n 4
		+	#SBATCH -t 1:00:00
		+	#SBATCH -p=compute
		+
		+	module load bowtie1/1.1.21 samtools/gcc/1.3.1
		+
		+	# Run bowtie
		+	bowtie dmel5 -p 4 /gpfs/data/shared/biomed/example_fastq/rna_seq/s1_r1.fastq -S s1_r1.sam
		+
		+	# Bowtie only give sam format output, if you need bam format, use samtools
		+	samtools view -bS s1_r1.sam > s1_r1.bam
	</pre>		</pre>

← Older revision		Revision as of 10:38, 16 November 2022
Line 52:		Line 52:
	* [http://bowtie-bio.sourceforge.net/tutorial.shtml http://bowtie-bio.sourceforge.net/tutorial.shtml]		* [http://bowtie-bio.sourceforge.net/tutorial.shtml http://bowtie-bio.sourceforge.net/tutorial.shtml]

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

@@ Line 44: / Line 44: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@login01 ~]$ module load bowtie1/1.1.21
+[username@login01 ~]$ module add bowtie1/1.1.21
 </pre>

@@ Line 52: / Line 52: @@
 * [http://bowtie-bio.sourceforge.net/tutorial.shtml http://bowtie-bio.sourceforge.net/tutorial.shtml]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 5: / Line 5: @@
 * Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
 * Version: 1.1.2
-* Modules: bowtie1/1.1.2
+* Modules: bowtie/1.1.2
 * Licence: Open source (Github)

← Older revision	Revision as of 08:16, 6 April 2017
(No difference)

@@ Line 1: / Line 1: @@
 ==Application Details==
@@ Line 37: / Line 39: @@
 * [[applications/Tophat|Tophat]]
 * [[applications/Samtools|Samtools]]
-* [[aaplications/Bowtie2|Bowtie2]]
+* [[applications/Bowtie2|Bowtie2]]
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@login01 ~]$ module load cufflinks/2.2.1
+[username@login01 ~]$ module load bowtie1/1.1.21
 </pre>