Cuffdiff
Cuffdiff takes several cufflinks results merged by cuffmerge and computes differential expression in the context of the merged data.
# a typical cuffdiff command.
cuffdiff -p 8 -q -u -N -o name-diff_out -b mm9.fa -L G1,G2 merged_asm/merged.gtf g1-s1/accepted_hits.bam,g1-s2/accepted_hits.bam g2-s1/accepted_hits.bam,g2-s2/accepted_hits.bam
In this example, 8 threads max are attributed to the job, the output is set to quiet, multi-read-correction is applied (-u), and upper-quartile-norm is requested (-N). For clarity, two groups are here compared and labelled (-L) 'G1' and 'G2'. Each group comprizes two samples (replicate) named g?-s1 and g?-s2 and their corresponding 'accepted_hits.bam' files are provided as a comma-separated list.
Note that no-space are added near the comma and that the two groups are separated by one space.
The result will be a new folder named 'name-diff_out' and containing a number of files describing the result of computing differential expression between the two sample groups.
-rwxrwx---. 1 root vboxsf 2.6M Nov 7 17:58 cds.count_tracking -rwxrwx---. 1 root vboxsf 2.2M Nov 7 17:58 cds.diff -rwxrwx---. 1 root vboxsf 5.5M Nov 7 17:58 cds_exp.diff -rwxrwx---. 1 root vboxsf 5.5M Nov 7 17:58 cds.fpkm_tracking -rwxrwx---. 1 root vboxsf 7.5M Nov 7 17:58 cds.read_group_tracking -rwxrwx---. 1 root vboxsf 4.3M Nov 7 17:58 gene_exp.diff -rwxrwx---. 1 root vboxsf 2.1M Nov 7 17:58 genes.count_tracking -rwxrwx---. 1 root vboxsf 4.6M Nov 7 17:58 genes.fpkm_tracking -rwxrwx---. 1 root vboxsf 6.2M Nov 7 17:58 genes.read_group_tracking -rwxrwx---. 1 root vboxsf 14M Nov 7 17:58 isoform_exp.diff -rwxrwx---. 1 root vboxsf 6.4M Nov 7 17:58 isoforms.count_tracking -rwxrwx---. 1 root vboxsf 16M Nov 7 17:58 isoforms.fpkm_tracking -rwxrwx---. 1 root vboxsf 20M Nov 7 17:58 isoforms.read_group_tracking -rwxrwx---. 1 root vboxsf 3.6M Nov 7 17:58 promoters.diff -rwxrwx---. 1 root vboxsf 396 Nov 7 17:58 read_groups.info -rwxrwx---. 1 root vboxsf 323 Nov 7 17:58 run.info -rwxrwx---. 1 root vboxsf 6.3M Nov 7 17:58 splicing.diff -rwxrwx---. 1 root vboxsf 7.6M Nov 7 17:58 tss_group_exp.diff -rwxrwx---. 1 root vboxsf 3.6M Nov 7 17:58 tss_groups.count_tracking -rwxrwx---. 1 root vboxsf 7.6M Nov 7 17:58 tss_groups.fpkm_tracking -rwxrwx---. 1 root vboxsf 11M Nov 7 17:58 tss_groups.read_group_tracking
