IGV: empty tracks?

[cnyh]

I am trying to load some .bam files into Integrated Genome Viewer. However, even when I zoom in to a particular gene that I've found to be differentially expressed in this data set, I don't see any reads at all. I'm not sure what I'm doing wrong, can anyone help?

Steps taken:
- collected .fq files from 3 biological replicates from each of 4 conditions, in total 12 samples
- mapped to Ensembl hg19 using tophat2
- merged each set of 3 bam files from each condition, into one collected bam file, using picard.
- indexed the bam files using samtools
- imported the annotation file and the four collected bam files into IGV
- zoomed in to individual genes, but see only blank tracks

[kopi-o]

I've seen empty tracks in IGV though there were actually alignments in the corresponding region. In one case the problem turned out to be that the BAM file wasn't sorted, in other cases the reason was not clear and the alignments became visible after restarting IGV.

[sBeier]

There is a setting in the preferences under the tab alignment, that determines from what mapping quality upwards the alignments are shown. Depending on how the alignments were produced, mapping quality might actually be not set, or set to either 0 or 1. Or it might just be generally bad. If then you have this parameter set to 20, the alignments will not be shown, although you still see there are alignments from the coverage track.

[wilson90]

Please check your chromosome. (is it NCBI genome or UCSC genome)

Hint:
NCBI: 1
UCSC: chr1

=)