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--- mkatari-bioinformatics-august-2013-bowtienotes [2014/04/30 12:26] – mkatari
+++ mkatari-bioinformatics-august-2013-bowtienotes [2014/04/30 12:29] – mkatari
@@ Line 1: / Line 1: @@
 [[mkatari-bioinformatics-august-2013|Back to Manny's Bioinformatics Workshop Home]]
-====== Bowtie on Cassava ======
+====== Creating and Running Bowtie using Cassava ======
+Make you are in "interactive mode"
 ) Download cassava genome from phytozome
+<code>
 wget ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/assembly/Mesculenta_147.fa.gz
+</code>
 ) created a directory called cassava
+<code>
 mkdir cassava
+</code>
 ) move fasta sequence in the directory
+<code>
 mv Mesculenta_147.fa.gz cassava/
+</code>
 ) uncompress using gunzip
+<code>
 cd cassava
 gunzip Meculenta_147.fa.gz
+</code>
 ) Count number of scaffold in the file
+<code>
 grep ">" Mesculenta_147.fa | wc
+</code>
 ) load bowtie module
+<code>
 module load bowtie2
+</code>
 ) Create the bowtie index.
+<code>
 bowtie2-build Mesculenta_147.fa cassava
+</code>
 ) Run Bowtie using single end fastq as input. See bowtie2 for instructions on how to run it on pair-end sequences.
+<code>
 bowtie2 -x cassava/cassava -U test.fastq -S test.sam
+</code>