Question: DEG from BAM file
0
gravatar for bioz
11 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 • 432 views
ADD COMMENTlink modified 11 months ago by WouterDeCoster43k • written 11 months ago by bioz10
2
gravatar for bharata1803
11 months ago by
bharata1803450
Japan
bharata1803450 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 months ago by bharata1803450
0
gravatar for WouterDeCoster
11 months ago by
Belgium
WouterDeCoster43k 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 months ago by WouterDeCoster43k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 693 users visited in the last hour