problem using samtools tview viewer

[lindseyjane]

Hello,

Has anyone had a problem using the samtools tview?

using the command

samtools tview sorted.bam ref.fa

I simply get a blank black screen and no display, no error message either.

Is this because the reference sequence is too big?
I have not had any problems before with tview but here I am trying to view an alignment against all 5 chromosomes rather than 1 chromosome at a time.
Any advice would be appreciated, thanks.

[nilshomer]

Hello,

Has anyone had a problem using the samtools tview?

using the command

samtools tview sorted.bam ref.fa

I simply get a blank black screen and no display, no error message either.

Is this because the reference sequence is too big?
I have not had any problems before with tview but here I am trying to view an alignment against all 5 chromosomes rather than 1 chromosome at a time.
Any advice would be appreciated, thanks.

A blank screen means at that position (the start) there are no reads. Try using the "?" key to get options to move around. Specifically, use "g" to specify a "chrosition" to which you wish to move.

[lindseyjane]

Thank you, problem solved

[maivantan]

can you tell how to solve the problem? Because I also got the same problem, it mean that when i used the command ''samtools tview 140222A2.sorted.bam ~/tan_analysis/IRGSP-1.0_genome.fasta''

the screening show ''NNNNNN'' all
Can you suggest please?

Thank you very much