How to visualize read depth based on genomic location

Question

[Whoknows]

Hi friends

I need a tool for creating a plot for of read depth distribution on genomic location Actually read distribution is important for me, the plot should discriminate depth in some area like TSS, TTS and gene.

I have design a sample plot, please see the image:

Answer 1

[Devon Ryan]

It sounds like you want plotProfile, plotHeatmap, or plotEnrichment from deepTools.

[Whoknows]

Thanks Devon, deeptools fits my question. But, can I specify TSS and TTS region for creating such plot? or I should define them based on my data by applying up/down stream length??

Thanks in advance.

[Devon Ryan]

Just give it a BED or GTF file and use the scale-regions mode in computeMatrix. It then defaults to TSS and TTS. If you want up/downstream regions as well, specify their lengths with -a ("after", or "downstream") and -b ("before", or "upstream").

Answer 2

[Whoknows]

This code works for me :

bamCoverage -b  accepted_hits.bam  -o T1.bw

computeMatrix reference-point   --referencePoint TSS  -b 200 -a 200  -R T.gtf  -S T1.bw  --skipZeros  -o T1_TSS.gz  --outFileSortedRegions T1_TSS_genes.bed 

plotProfile    -m T1_TSS.gz   -out T1_TSS.png  --plotType=fill   --plotTitle "T1"

Answer 3

[Chirag Nepal]

There are many such tools.

Here is one with good user interface EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)

There are multiple unix based (such as deeptools, ngs plot and ..)

[Whoknows]

Thanks Chirag, Actually my bed files are too big, > ~12G ; I'm afraid I could not use them in windows.

[Devon Ryan]

How big is your genome if the BED files are 12 or so gigs? That's vastly larger than the human annotation, which is the most complete one out there!

[Whoknows]

Actually the genome is very small ,but I've made bed files by merging 3 biological replicates bam files into 1 bam and then I made Bed, which makes them really large.

I have used samtools merge and then bedtools bamToBed for creating my bed files.

[Devon Ryan]

Delete the BED files, they're of no use. Use only the BAM file(s).

[Whoknows]

Yes, thats true How can I use BAM files, I need to merge my bam replicates. Is the following way right?

I discard BED files and I just used genome GTF file for -R option, with bigwig files which made from samtools merge bam > .bw via bamcoverage tool.

[Devon Ryan]

Yup, that should work much better.