Bowtie on Helix
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).
Bowtie was developed by Langmead et al at the University of Maryland. Bowtie reference
Programs location
/usr/local/apps/bowtie
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
[user@helix]$ module avail bowtie ------------- /usr/local/Modules/3.2.9/modulefiles -----------------------
bowtie/0.12.8 bowtie/2-2.0.0-beta7 bowtie/2-2.0.2(default)
[user@helix]$ module load bowtie [user@helix]$ module list Currently Loaded Modulefiles: 1) bowtie/2-2.0.2 [user@helix]$ module unload bowtie [user@helix]$ module load bowtie/0.12.8 [user@helix]$ module list Currently Loaded Modulefiles: 1) bowtie/0.12.8 [user@helix]$ module show bowtie ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/bowtie/2-2.0.2: module-whatis Sets up bowtie2-2.0.2 prepend-path PATH /usr/local/apps/bowtie/2-2.0.2 -------------------------------------------------------------------
The iGenomes is available on helix/biowulf in /fdb/igenomes. Illumina has provided the RNA-Seq user community with a set of genome sequence indexes (including Bowtie indexes) as well as GTF transcript annotation files called iGenomes. These files can be used with TopHat and Cufflinks to quickly perform expression analysis and gene discovery. The annotation files are augmented with the tss_id and p_id GTF attributes that Cufflinks needs to perform differential splicing, CDS output, and promoter user analysis. Prebuilt bwa, bowtie, and bowtie2 indexes can be found under 'Sequence' subdirectory of each organism.
Bowtie can be run multi-threaded. However, do not do that on Helix. Do not use -p flag on helix. On the other hand, users can take advantage of it by running Bowtie on Biowulf cluster.
How To Use
All examples below are using the hg19 index files located under /fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index :
Example 1
$ cd /home/$USER/bowtie $ module load bowtie $ bowtie2 -t -x /fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome \ -1 reads/ABCD_1000_1.fq -2 reads/ABCD_1000_2.fq -S out.sam 1-:<0,148810,2> 1-:<0,2852852,1> 1-:<0,4930433,2> 1-:<0,905664,2> 1+:<0,1093035,2> Reported 5 alignments to 1 output stream(s)
- -t : print timing statistics
- -x genome: the basename of the index for the genome to be searched in $BOWTIE2_INDEXES. Since $BOWTIE2_INDEXES has been set, the hg19 indexes (the basename of the index files in that directory is 'genome') from that directory will be used. NOTE, use $BOWTIE_INDEXES instead of $BOWTIE2_INDEXES if running bowtie earlier than 2.0 version. The 'module load bowtie' above load default version bowtie2.
- -1, -2 reads/ABCD_1000_*.fq: the Fastq file containing the reads
- -S out.sam: output file for the alignments.
