mkatari-bioinformatics-august-2013-bowtienotes
Differences
This shows you the differences between two versions of the page.
Next revision | Previous revisionLast revisionBoth sides next revision | ||
mkatari-bioinformatics-august-2013-bowtienotes [2014/04/30 12:24] – created mkatari | mkatari-bioinformatics-august-2013-bowtienotes [2014/04/30 12:29] – mkatari | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | #Bowtie | + | [[mkatari-bioinformatics-august-2013|Back to Manny' |
+ | |||
+ | ====== Creating and Running | ||
+ | |||
+ | Make you are in " | ||
1) Download cassava genome from phytozome | 1) Download cassava genome from phytozome | ||
+ | < | ||
wget ftp:// | wget ftp:// | ||
+ | </ | ||
2) created a directory called cassava | 2) created a directory called cassava | ||
+ | < | ||
mkdir cassava | mkdir cassava | ||
+ | </ | ||
3) move fasta sequence in the directory | 3) move fasta sequence in the directory | ||
+ | < | ||
mv Mesculenta_147.fa.gz cassava/ | mv Mesculenta_147.fa.gz cassava/ | ||
+ | </ | ||
4) uncompress using gunzip | 4) uncompress using gunzip | ||
+ | < | ||
cd cassava | cd cassava | ||
gunzip Meculenta_147.fa.gz | gunzip Meculenta_147.fa.gz | ||
+ | </ | ||
5) Count number of scaffold in the file | 5) Count number of scaffold in the file | ||
+ | < | ||
grep ">" | grep ">" | ||
+ | </ | ||
6) load bowtie module | 6) load bowtie module | ||
+ | < | ||
module load bowtie2 | module load bowtie2 | ||
+ | </ | ||
7) Create the bowtie index. | 7) Create the bowtie index. | ||
+ | < | ||
bowtie2-build Mesculenta_147.fa cassava | bowtie2-build Mesculenta_147.fa cassava | ||
+ | </ | ||
8) Run Bowtie using single end fastq as input. See bowtie2 for instructions on how to run it on pair-end sequences. | 8) Run Bowtie using single end fastq as input. See bowtie2 for instructions on how to run it on pair-end sequences. | ||
+ | < | ||
bowtie2 -x cassava/ | bowtie2 -x cassava/ | ||
+ | </ |
mkatari-bioinformatics-august-2013-bowtienotes.txt · Last modified: 2014/07/03 13:19 by mkatari