Quick Visual Inspection Of Mapping Images For A List Of Regions

Question

[2184687-1231-83-]

Hi,

I would like to quickly have a look to a few hundred images of reads mapped to a reference, for a list of a few hundred regions.

What I've got so far is a file with a list of regions "chrname:start-end", and I am simply using samtools tview for them like this:

cat peaks.txt | while read i; do echo -e "g$i\n." | samtools tview my.bam my.ref.fa.gz; done

The "." at the end is to switch of the dots in the tview configuration. I use Ctrl+C to go to the next region.

Is there a better way to do this? Maybe something that generates image files?

Cheers

Answer 1

[Sean Davis]

Take a look at the IGV browser. In particular, it has some nice scripting functionality:

http://www.broadinstitute.org/software/igv/batch

and

http://www.broadinstitute.org/software/igv/PortCommands

[Aaronquinlan]

bedtools has a script called bedToIgv that will create an IGV batch script for generating images for each interval in a BED/GFF/VCF file.

[Pierre Lindenbaum]

+1 for the batch query

Answer 2

[Scott Cain]

Since you already have BAM files, you can use Bio::DB::Sam with GBrowse and gbrowse_img to generate images. It could easily be scripted using wget or curl and shell scripting and gbrowse_img will return graphics like GBrowse would use. Alternatively, you could skip the webserver and do the image generation with Bio::Graphics and perl. For more information, you can take a look at:

GBrowse2 Install Doc

Bio::DB::Sam

Bio::Graphics

BioPerl

Answer 3

[Ido Tamir]

same answer as for other thread

most genome browsers have scripting capability IGB and IGV.[?] GBrowse2 also allows linking and by this scripting.

If you want something really small:[?]

1. download the two files from lookseq lookseq
2. and compile them: g++ render_image.cpp -O3 -o render_image -lpng -L . -lbam
3. create image with: ./render_image --bam=mybam.bam --options=snps,pairs,arrows,single,faceaway,inversions,linkpairs,colordepth --ref=myref.fa --region="2L:1-200000" --png=2L.a.png

This way you can quickly create small images with the reads from your bam file with many viewing options. like this example (click on one button on the right).

[Ido Tamir]

IIRC now I copied the lookseq files into the folder of the samtools and compile there for correct linkage with libbam YMMV.

Answer 4

[2184687-1231-83-]

For different level of zoomed-out views as bitmaps, Lookseq's render_image is great. In combination with ImageMagick's montage tool, it does pretty much all I want:

montage -tile 1 -geometry +0+0 $i/*.png $i.png

For nucleotide-level textual views, I've just been made aware about Pierre's bamttview, which is a modification of samtools tview:

http://plindenbaum.blogspot.com/2011/07/text-alignment-viewer-using-samtools.html

[2184687-1231-83-]

many thanks to the LookSeq people and @Pierre Lindenbaum for both solutions.