I have a smaller data set from an Illumina Solexa (~20-30 GB) and my group has been running some comparative analysis using both CLC Genomeworkbench and Bowtie. The problem we have experienced is the issue of viewing the alignments from Bowtie. The files were converted to SAM format from Bowtie but are too big to use the sam2bed.py script posted on here. I had considered splitting the files but worry about splitting the alignments. Our files can be converted to BAM or bigbed format but then require an HTTP/FTP accessible folder that we do not have, nor can they be viewed with another open souce viewer. Is there an effective, and I dare say easy, way to visualize the alignment using an open source viewer? I am not a novice at bioinformatics but it seems that if you have a significantly sized data set than you are going to be up a creek when attempting to visualize them if you do not have a major computational framework.
Any help is appreciated.
Any help is appreciated.
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