I have 4 fastq files. From some earlier post I tried to analysethrough Galaxy sever.
I used "fastp", "clip adapter" and also "trimomatic" separately three different times to trim adapter.
As I have paired end data, I then joined the output of R1 and R2 using "FASTQjoiner" , "fastqjoin" , and "fastqinterlacer" separately three different times.
Then I aligned using Bowtie2 (against all three time) and compared using "EdgeR" and "Deseq2" separately from three different output.
I also annotate after I got differential expression both time using mice genome .gff file.
But I am not able to get a excel file having Gene name and Q-value. I am getting html with tabular result having gene ID, log2fold change, p value, st error etc. but NO Q value and gene name.
Also when I am trying to make heat map using ggplot or heatmap2 it is showing weird plot.
Can anyone tell me if I am doing wrong in work flow, and whether for that the gene ID and heat map problem is occuring.
Thanks in advance!!
Best,
Somenath
Yes there are other columns also including FDR.
Could you tell me how to proceed from there and where is the Q value?