mkatari-bioinformatics-august-2013-bowtienotes
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mkatari-bioinformatics-august-2013-bowtienotes [2014/04/30 12:24] – created mkatari | mkatari-bioinformatics-august-2013-bowtienotes [2014/07/03 13:19] (current) – mkatari | ||
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- | #Bowtie on Cassava | + | [[mkatari-bioinformatics-august-2013|Back to Manny' |
- | 1) Download cassava genome from phytozome | + | ====== Creating a Bowtie Index and Performing an alignment using Cassava as a reference ====== |
- | wget ftp://ftp.jgi-psf.org/ | + | 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. |
- | 2) created | + | 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 |
- | mkdir cassava | + | |
- | 3) move fasta sequence in the directory | + | So first steps are to create |
- | mv Mesculenta_147.fa.gz cassava/ | + | |
+ | < | ||
+ | mkdir ~/cassava | ||
- | 4) uncompress using gunzip | ||
cd cassava | cd cassava | ||
+ | |||
+ | wget ftp:// | ||
+ | </ | ||
+ | |||
+ | Now we will uncompress the file using gunzip | ||
+ | |||
+ | < | ||
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 ">" | + | |
- | 6) load bowtie | + | < |
+ | grep ">" | ||
+ | </ | ||
+ | |||
+ | In order to use Bowtie2 commands we have to first load the module | ||
+ | |||
+ | < | ||
module load bowtie2 | module load bowtie2 | ||
+ | </ | ||
+ | |||
+ | In order to create the index, which will be used like a database when we are aligning the reads to the reference, we use the command bowtie2-build. For cassava this should take about 10 minutes. | ||
- | 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 | + | 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.1398860646.txt.gz · Last modified: 2014/04/30 12:24 by mkatari