Question: DEG from BAM file
0
gravatar for bioz
11 days ago by
bioz0
bioz0 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 • 115 views
ADD COMMENTlink modified 11 days ago by WouterDeCoster37k • written 11 days ago by bioz0
2
gravatar for bharata1803
11 days ago by
bharata1803420
Japan
bharata1803420 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 11 days ago by bharata1803420
0
gravatar for WouterDeCoster
11 days ago by
Belgium
WouterDeCoster37k 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 11 days ago by WouterDeCoster37k
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