Hi,I had problem with using CummeRbund to analyse the output from Cuffdiff.
I was trying to analysis RNA-seq using Cufflinks (I mean the suite) .
I got the BAM file after using Tophat and Bowtie for mapping.
Since I am not interested in splicing variants this time, so I skipped using Cufflinks(the programme) and Cuffmerge, directly move to Cuffdiff with BAM file, like the workflow hightlighted in bright blue here https://wikis.utexas.edu/display/bioiteam/Introduction+to+tophat+cufflinks+workflow
Since I could not successfully install CummeRbund on my server: https://support.bioconductor.org/p/73617/
So I decided to analyse and plot with CummeRbund on my Mac, installed CummeRbund and copy all the output files from my server.
but when I input command:
>cuff<-readCufflinks() # which are supposed to automatically find the default files and begin parsing my data >cuff # Nothing was done. CuffSet instance with: 0 samples 0 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS
when I tried to test the readCufflinks command using the test dataset
> cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund")) > cuff # it seems that it worked. CuffSet instance with: 3 samples 400 genes 1203 isoforms 662 TSS 906 CDS 1062 promoters 1986 splicing 990 relCDS
Then I wonder whether the Cuffdiff was carried out successfully or not, so I checked gene_exp.diff by
cat gene_exp.diff test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant NM_001001130 NM_001001130 - chr13:67830198-67857775 q1 q2 OK 5.07206 9.76439 0.944959 1.37033 0.1484 0.869478 no NM_001001144 NM_001001144 - chr9:110235791-110287453 q1 q2 OK 7.58925 7.62 0.00583411 0.00620651 0.99445 0.998025 no NM_001001152 NM_001001152 - chr13:67355853-67370004 q1 q2 OK 1.04851 1.34624 0.36059 0.373615 0.7031 0.973148 no NM_001001160 NM_001001160 - chr6:85419569-85452988 q1 q2 NOTEST 6.48556e-05 8.73562e-05 0
it seems to me that Cuffdiff worked.
So I have no clue about what went wrong and how to move on.
Can anyone have any suggestions?
If any further information is need to evaluate the problem, please kindly let me know.