[billstevens]

Thanks I'll give that a try.

[jiewencai]

It‘s so hard for me to understand those answers.

[Gonza]

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
G

[GenoMax]

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
G

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.

[Gonza]

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.