mkatari-bioinformatics-august-2013-bowtienotes
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mkatari-bioinformatics-august-2013-bowtienotes [2014/04/30 12:29] – mkatari | mkatari-bioinformatics-august-2013-bowtienotes [2014/07/03 13:19] (current) – mkatari | ||
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[[mkatari-bioinformatics-august-2013|Back to Manny' | [[mkatari-bioinformatics-august-2013|Back to Manny' | ||
- | ====== Creating | + | ====== Creating |
- | Make you are in "interactive mode" | + | This is a quick example of how to build a bowtie index and executing bowtie. Normally you will create the index only once you there is no need to create a special script for it. Just make sure you are in **interactive mode** mode and we can do everything on the command line. |
- | 1) Download | + | Once you have found the sequence on the web you want to use as a reference you can use the linux command wget to download it quickly. And to make sure we keep our data organized, let's create a directory called **cassava** where we will store the file. |
+ | |||
+ | So first steps are to create the directory and download the file. | ||
< | < | ||
+ | mkdir ~/cassava | ||
+ | |||
+ | cd cassava | ||
+ | |||
wget ftp:// | wget ftp:// | ||
</ | </ | ||
- | 2) created a directory called cassava | + | Now we will uncompress the file using gunzip |
- | < | + | |
- | mkdir cassava | + | |
- | </ | + | |
- | 3) move fasta sequence in the directory | ||
< | < | ||
- | mv Mesculenta_147.fa.gz cassava/ | ||
- | </ | ||
- | 4) uncompress using gunzip | ||
- | < | ||
- | cd cassava | ||
gunzip Meculenta_147.fa.gz | gunzip Meculenta_147.fa.gz | ||
</ | </ | ||
- | 5) Count number of scaffold | + | |
+ | To see how many scaffolds we in our file we can **grep** for the greater-than sign and then using the command **wc** to count lines. | ||
< | < | ||
- | grep ">" | + | grep ">" |
</ | </ | ||
- | 6) load bowtie | + | |
+ | In order to use Bowtie2 commands we have to first load the module | ||
< | < | ||
module load bowtie2 | module load bowtie2 | ||
</ | </ | ||
- | 7) Create | + | |
+ | In order to create | ||
< | < | ||
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 | + | |
+ | Based on the the type of sequences you have ( single end or pair end ) the options | ||
+ | See the link for [[http:// | ||
< | < | ||
bowtie2 -x cassava/ | bowtie2 -x cassava/ | ||
</ | </ |
mkatari-bioinformatics-august-2013-bowtienotes.1398860981.txt.gz · Last modified: 2014/04/30 12:29 by mkatari