I would like to make a picture of a bam file aligned at a specific region. Something similar than samtools tview but as a picture not as a text output :
Do you know any tools for doing this ?
•
written
by
sacha
2 answers
ImageMagick is always the answer to anything image-automation related :)
samtools tview your.bam -p chr1:5477604 -d text | convert -background black -fill white label:@- out.png
if you don't have 'convert' then just install ImageMagick.On OSX that's brew install imagemagick
IGV can be driven by a batch script, and therefore command line. It's a little bit of work to get the script written where you need it, but then you get very nice diagrams how you like them. Should be doable in Bash.
Their scripting interface looks like a series of commands, open this bam, sort the reads that way, go to this location, then take a "screenshot". It can all happen behind the scenes, and result in just the picture you are looking for.
Log in to answer this question.
-
samtools mpileup and samtools tview give different reads quality results
written by cocoboxt •
-
Mapping reads to 5 UTR, 3 UTR and CDS
written by student12 •
-
Different coverage depth
written by wes •
-
How to make Q-Q plots for different models at a single chart using R?
written by rimgubaev
-
Is there a limit for SAMTOOLS tview option?
written by bioplanet •
-
Duplicates on Illumina
written by predeus
-
Visualization of ChIP-seq data (mapped reads)
written by Wet&DryImmunology
-
Why this SNV (chr5:161300148-161300148) is G in BioMuta Database ,rather than T or A from Ensembl…
written by winter_li •
-
overlapping texts (plot.PCA in FactoMineR)
written by mbk0asis
-
How To Add Additional Panes To A Clustering Heatmap Plot Created With R
written by Jonathan Crowther
Automated or interactive? Most genome browsers (IGV etc) will export images in various formats.