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Old 05-17-2015, 05:56 AM   #7
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Originally Posted by rodrigo.duarte88 View Post
Ah!! This is what I needed to know!! Yes, I am trying to align my reads to a specific part of the chromosome due to computational limitations..
There are two ways of doing this as I alluded to above.

1. Doing the alignment to the entire genome followed by the samtools view option to extract a particular region would be more straightforward (with a sorted and indexed bam file).
$ samtools view your.bam chr1:10000-20000
2. If you really want to work with just the region of interest then (using the iGenomes file bundle)
a. Get that sequence from the "genome.fa" (use the appropriate chromosome sequence from this file) using the bedtools "getfasta" option:
b. Create appropriate indexes (bowtie/bowtie2) using this file.
c. Select appropriate regions from the GTF file. You will have to adjust the coordinates appropriately (not sure how big a region you are looking at).
Accomplishing a and b is straightforward. c would be difficult.
3. You could use BioMart or UCSC table browser to extract the sequence and the annotations. Make the indexes using that sequence file.

Unless you are really constrained for computational power going with option 1 is straightforward.

Last edited by GenoMax; 05-17-2015 at 06:01 AM.
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