Question: How to find the differences in aligned bam files
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gravatar for krushnach80
3.1 years ago by
krushnach80690
krushnach80690 wrote:

I have a set of RNA -seq data , I have aligned them ,have the accepted.bam file, to view the coverage i'm using the IGV tools but it seems there is something wrong with the sample or sequencing if I see there are differences kind stark differences between the replicates at certain places both of them are control.Is there a way to do absolute quantification of both the aligned files .Since both of them are bam files , is it possible to compare both the bam files and get the difference.

Any suggestion or help would be highly appreciated

rna-seq • 1.3k views
ADD COMMENTlink written 3.1 years ago by krushnach80690

Probably, but you'll need to exactly define what you want to compare.

ADD REPLYlink written 3.1 years ago by Devon Ryan94k

I just want to make sure like there are no major differences in the replicates overall. I read about deeptools which has this bamCompare function , can i use that to see if there is a differences ?

ADD REPLYlink written 3.1 years ago by krushnach80690

If you really want to do this with the BAM files rather than the counts, then use multiBamSummary from deepTools followed by plotPCA or similar.

ADD REPLYlink written 3.1 years ago by Devon Ryan94k

okay i dud use the bam compare but now i will give multiBamSummary a try and PCA

ADD REPLYlink written 3.1 years ago by krushnach80690

Do you want to count reads per gene?

ADD REPLYlink written 3.1 years ago by WouterDeCoster43k

yes I would like to do that counts read per gene from both the set

ADD REPLYlink written 3.1 years ago by krushnach80690

Then you can use software like htseq-count and featureCounts.

ADD REPLYlink written 3.1 years ago by WouterDeCoster43k

yes I have taken out read counts using featurecounts .So what would be the next step?

ADD REPLYlink written 3.1 years ago by krushnach80690

Differential expression analysis using e.g. DESeq2.

ADD REPLYlink written 3.1 years ago by WouterDeCoster43k
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