Hi all,
I have two RNA-Seq samples. Calculating p-value for two samples is not possible. So, I want to calculate fold change for Sample1 vs Sample2.
Based on that I want to detect differential expressed genes.
Each sample has the following information.
tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status
Can anyone tell me how can I do that for that samples?
Is there any R package to calculate FC for two smaples?
1 answer
Look at Cuffdiff . The information you gave suggests that cufflinks was used. There are other tools to read in FPKM values but Cuffdiff would be a good starting point
http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#cuffdiff-input-files
Log in to answer this question.
-
Genes' fpkm values through cufflink
written by arsala521 •
-
#Cufflinks# Can I change the tracking id?
written by hyeonjin •
-
cufflink output FPKM values
written by blooming.daisy333 •
-
Cufflinks output fewer features than the annoation file.
written by --panda-- •
-
cufflinks results is all zeros...??
written by sa1987 •
-
no XLOC gene_id or TCONS transcript_id in fpkm_tracking files
written by jolin0701-dy
-
cufflinks with reference annotation, FPKM for a gene
written by tonja.r
-
cufflinks output file isoforms.fpkm_tracking has mixed ENSGxxx and ENSTxxx ID in the tracking_id co…
written by Xianjun
-
How To Stated Out Name Of Gene In Cufflink Genes.Fpkm_Tracking
written by smagikern •
-
Error Running Cuffmerge Without Reference Gtf Or Fasta File
written by bio monkey •
