Create Image From Mapping Region

Question

[Yahan]

I am looking for a way to generate an image for a set of mapping positions in a bam file.

Instead of browsing to each position by providing the coordinates in a tool like samtools tview, which is pretty cumbersome, I could then provide a list of such coordinates after which for each of them an image would be created.

Then I could browse these images to get a first impression of how the mapping looks like.

Does anyone know of a tool that could do something like that?

Thanks

Answer 1

[Pierre Lindenbaum]

I wrote something like this for IGV: http://plindenbaum.blogspot.fr/2011/07/controlling-igv-through-port-my.html

and I also wrote a tool that takes a VCF input and a bam: see http://code.google.com/p/variationtoolkit/wiki/VcfTTView

$ echo -e "ref\t3\nref2\t2" |\
  vcfttview -x 3 -B toy.bam -R toy.fa

>ref:3

1         11              21        31         41        51        61           
AGCATGTTAGATAA****GATA**GCTGTGCTAGTAGGCAG*TCAGCGCCATNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      ........    ....  ......K.K......K. ..........                            
      ........AGAG....***...      ,,,,,    ,,,,,,,,,                            
        ......GG**....AA                                                        
        ..C...**** ...**...>>>>>>>>>>>>>>T.....                                 



>ref2:2

1         11            21        31        41        51        61              
aggttttataaaac****aattaagtctacagagcaactacgcgNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
.............Y    ..W...................                                        
..............****..A...                                                        
 .............****..A...T.                                                      
     .........AAAT.............                                                 
         C...T****....................                                          
           ..T****.....................                                         
             T****......................

Answer 2

[Sean Davis]

You can use IGV and talk to IGV via its port mechanism. If you are an R user, the SRAdb package has convenience functions to work with IGV to produce plots.

Answer 3

[Fidel]

I've found that the best way to achieve what you want is using IGV batch script.

You can quickly generate a batch script as follows:

> echo "snapshotDirectory <some directory to put the images>" > igv_batch_script.txt
> cat file.bed | perl -lane 'print "goto $F[0]:$F[1]-$F[2]\nsnapshot";' >>  igv_batch_script.txt

Then you just load this file in IGV: "File" -> "Run Batch Script..."

For further info look at: http://www.broadinstitute.org/igv/batch

Answer 4

[Alex Reynolds]

If you are familiar with the UCSC browser, you could load your reads into a custom track, add annotation tracks (if desired) and use UCSC Fetch to generate screenshots around regions-of-interest.

You could then use something like SimpleViewer to make a quickly-browsable gallery.