Thanks I'll give that a try.
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It‘s so hard for me to understand those answers.Comment
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Hi All,
I converted the .bam file to .bai file using
$ samtools index test_sorted.bam test_sorted.bai (and now I have both in the same folder). When i upload the .bam file to IGV it seems to work, but i see no alignment of the reads against the genome (i do see the genome in blue)
I am using the TAIR10 genome.
what could be this? ideas?
many thanks
GLast edited by Gonza; 10-17-2014, 09:14 AM.Comment
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Chromosome names need to match between your BAM/genome in IGV (I assume you are using the built-in genome) in order for IGV to be able to display your data. Other possibility is you need to start zooming in/out/sideways depending on the relative location of IGV display, to see the mapped reads.Originally posted by Gonza View PostComment
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Thanks, I just realized that you need to start scrolling to the side to see where the reads are. It wasn't really intuitive....sorry for the silly question.Comment
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