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
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
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