DEG from BAM file
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2.7 years ago
bioz ▴ 20

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 ?

RNA-Seq deg gene R • 1.2k views
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2.7 years ago
bharata1803 ▴ 530

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.

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2.7 years ago

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.

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