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Just got result from cufflinks but not quite understand the output genes.fpkm_tracking:
I used this command:
I then wish to check the estimated expression for genes annotated in the refFlat GTF files, but found only around 6000 genes (with known gene symbols) were reported in genes.fpkm_tracking, while the remaining are all with ids like CUFF.XXX, see below...
So I was just wondering how I could know the expression of all ~20000 genes in the refFlat annotation files (such as Notch1, FOXD1,..), and how can I convert CUFF.xxx into each gene? It's unlikely that all the CUFF.xxx are novel transcripts, right?
Thank you for your advice on it
### the output####
I used this command:
Code:
cufflinks -o Result -p 4 -g $GTF -b $RefGenome -u $file
So I was just wondering how I could know the expression of all ~20000 genes in the refFlat annotation files (such as Notch1, FOXD1,..), and how can I convert CUFF.xxx into each gene? It's unlikely that all the CUFF.xxx are novel transcripts, right?
Thank you for your advice on it
### the output####
Code:
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 OR4F5 - - OR4F5 - - chr1:69090-70008 - - 0 0 0 OK CUFF.4 - - CUFF.4 - - chr1:109920-110286 - - 1.57124 0.830549 2.31193 OK FAM138A - - FAM138A - - chr1:34610-36081 - - 0 0 0 OK CUFF.6 - - CUFF.6 - - chr1:126628-127545 - - 0.207493 0.0923964 0.322589 OK CUFF.5 - - CUFF.5 - - chr1:125397-125894 - - 0.804427 0.435331 1.17352 OK CUFF.8 - - CUFF.8 - - chr1:167776-168206 - - 1.66698 1.04788 2.28608 OK CUFF.10 - - CUFF.10 - - chr1:163967-164488 - - 0.425551 0.168934 0.682169 OK CUFF.9 - - CUFF.9 - - chr1:169060-169232 - - 1225.18 702.763 1747.6 OK CUFF.11 - - CUFF.11 - - chr1:227422-227796 - - 7.54204 5.96942 9.11467 OK CUFF.12 - - CUFF.12 - - chr1:233147-233979 - - 0.292227 0.146113 0.43834 OK CUFF.13 - - CUFF.13 - - chr1:234725-235592 - - 0.379276 0.217552 0.540999 OK CUFF.14 - - CUFF.14 - - chr1:234090-234614 - - 0.612381 0.306191 0.918572 OK