Hi everyone
I used the HTSEQ package to count the reads. The output of this package was as follow:
Is this output format correct? Is the first column the gene id and the second column is the reads values?
If this format is correct, what should I do to calculate the expression values In the next step??
Hi Fahime,
It is correct.
If you meant Differential expression value, first you should filter your count table, then based on your design matrix apply comparison between your exprimental groups.
If you want to find RPKM,FPKM,TPM, you can use different way.
_ use STRING or RSEM for finding count table. Then their out put are containing expression value.
_ use cuff tools.
_ based on out put of HTSeq, first find length of each gene ( non overlap exonic regions) , then normalize number of reads based on library and then normalize based on gene length (for RPKM), and the other way around for TPM.
_ also you can use edgeR for RPKM.
Thanks Soheil Yousefi
I used Hatsaq. What should I do to calculate the length of each gene now?
I want to use the NOIseq Package. But I was confused about how to calculate the length of a gene and ...
Can you help me more?
To find gene length, you need to sum up the length of each non-overlap exonic regions for each gene.
You can use one of the below comments:
* Here, I have considered HG38
###1 )
library(GenomicRanges)
library(IRanges)
library(rtracklayer)
library(Rsamtools)
GTFfile = "Homo_sapiens.GRCh38.92.gtf"
FASTAfile = "Homo_sapiens_GRCh38.fa"
#Load the annotation and reduce it
GTF
thanks Soheil Yousefi
I used your command But there is an error, The output file is not correct also!
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