Question: DEG from BAM file
0
gravatar for bioz
9 months ago by
bioz10
bioz10 wrote:

Hi, I have an alignment file in bam format from STAR aligner. I want to study Differential expression gens from this bam file, I need all informations like p-value fold-change triplicate values ECT for plotting heat map and volcano.

Is it possible to make these plots from alignment bam file ?

deg rna-seq R gene • 356 views
ADD COMMENTlink modified 9 months ago by WouterDeCoster42k • written 9 months ago by bioz10
2
gravatar for bharata1803
9 months ago by
bharata1803440
Japan
bharata1803440 wrote:

To do DEG analysis, what you need is a readcount table. So, you just need read count software that accept BAM files. Try HTSeq count or featureCount. After you get read count table, you can do DEG using popular library like DESeq2, EdgeR, or limma/voom.

ADD COMMENTlink written 9 months ago by bharata1803440
0
gravatar for WouterDeCoster
9 months ago by
Belgium
WouterDeCoster42k wrote:

Please follow this workflow: https://www.bioconductor.org/help/course-materials/2017/CSAMA/labs/2-tuesday/lab-03-rnaseq/rnaseqGene_CSAMA2017.html

But I hope you have more than one bam - with just one sample you cannot do differential expression analysis.

ADD COMMENTlink written 9 months ago by WouterDeCoster42k
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