DEG from BAM file

Question

[bioz]

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 ?

Answer 1

[bharata1803]

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.

Answer 2

[WouterDeCoster]

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.