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Old 03-11-2015, 12:43 PM   #1
netpumber
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Default Bam file visualization through console

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.
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Old 03-11-2015, 01:13 PM   #2
dpryan
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samtools tview
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Old 03-11-2015, 01:41 PM   #3
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Thank you!
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Old 03-11-2015, 01:47 PM   #4
GenoMax
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Does it have X11? So you could use that to export graphical output to your local desktop.
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Old 03-12-2015, 05:06 AM   #5
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NO it doesn't have X11. Also when i m trying to use the samtools tview returns me that error


Quote:
[bam_index_load] fail to load BAM index.
Cannot read index for 'accepted_hits.bam'
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Old 03-12-2015, 05:14 AM   #6
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Just index the file then (samtools index). You'll need to sort it (samtools sort) if that wasn't already done.
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Old 03-12-2015, 12:17 PM   #7
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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 ?
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Old 03-12-2015, 12:47 PM   #8
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What are the parameters you used?
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Old 03-12-2015, 03:10 PM   #9
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Results are from tophat2.

Code:
samtools sort accepted_hints.bam accepted_hints.sort
samtools index accepted_hints.sort.bam 
samtools tview accepted_hints.sort.bam pathtogenome.fa
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Old 03-13-2015, 12:15 AM   #10
dpryan
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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).
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Old 03-13-2015, 04:08 AM   #11
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Ok. Thank you. Seems to work.
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