Hello Christian,

I found this FAQ on the IGV web site. They may be the best resource for resolving display issues if they continue. Comparing results between IGV and Galaxy's visualization tool Trackster can help you to determine the root cause of the problem.
http://www.broadinstitute.org/software/igv/BAM
http://www.broadinstitute.org/igv/FAQ

Hopefully this helps point you in the right direction,

Best,

Jen
Galaxy team

On 7/31/11 6:04 PM, Cristian Rojas wrote:

Hi people, I have a litle problem with Bowtie alignments. I am tryin to
align sRNA Illumina dataset to hairpin mirbase. The problem is that
after the steps (detailed below) I only obtain reads of 15-18nt, and I
know that I have a lot of microRNAs (20-22nt) in my data. Beside the
size problem, I realized that when the reads and the reference (the
precursor in any case) the sequences don't match as I would expect.
The sequential steps that I've made:
- Groom
- Clip (adaptor elimination)
- Bowtie against hairpin database (mirBase precursor)
- SAM-to-BAM
- Download Bam and Bai files
- Open in IGV the file and the hairpin database

May be I am doing something really bad, but I dont know. Any
help/suggestion/tip?
Thanks in advance


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