Bam file visualization through console

[netpumber]

Hello!

The linux server where i working on, hasn't any graphical interface, and i would like to ask, if there is any tool that visualize .bam files through console.

Thank you.

[dpryan]

samtools tview

[netpumber]

Thank you!

[GenoMax]

Does it have X11? So you could use that to export graphical output to your local desktop.

[netpumber]

NO it doesn't have X11. Also when i m trying to use the samtools tview returns me that error

[bam_index_load] fail to load BAM index.
Cannot read index for 'accepted_hits.bam'

[dpryan]

Just index the file then (samtools index). You'll need to sort it (samtools sort) if that wasn't already done.

[netpumber]

I sorted them, indexed them and when i tried to run tview with .sort.bam file and genome.fa, it returned a huge line only with NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNs.

Any idea ?

[Richard Finney]

What are the parameters you used?

[netpumber]

Results are from tophat2.

samtools sort accepted_hints.bam accepted_hints.sort
samtools index accepted_hints.sort.bam 
samtools tview accepted_hints.sort.bam pathtogenome.fa

[dpryan]

You probably want to use the -p option with a position. By default, you start at base 1 of the first contig/chromosome. If there are no alignments there, then you won't see anything except whatever the reference sequence is (if this is for a mammal, then typically a bunch of Ns).

[netpumber]

Ok. Thank you. Seems to work.