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How to visualize read depth based on genomic location

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:

enter image description here

tophat bed bigwig rna-seq
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written by Whoknows Whoknows

3 answers

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

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written by Devon Ryan Devon Ryan

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.

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written by Whoknows Whoknows

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").

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written by Devon Ryan Devon Ryan

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"
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written by Whoknows Whoknows

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 ..)

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written by Chirag Nepal Chirag Nepal

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

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written by Whoknows Whoknows

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!

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written by Devon Ryan Devon Ryan

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.

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written by Whoknows Whoknows

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

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written by Devon Ryan Devon Ryan

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.

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written by Whoknows Whoknows

Yup, that should work much better.

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written by Devon Ryan Devon Ryan

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