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Question: Cufflinks Cuffdiff - interpreting XLOC versus Gene/Transcript assignment when reference annotation was used
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gravatar for abcxyz5678
4 months ago by
abcxyz5678 • 0
abcxyz5678 • 0 wrote:

Hi everybody, I got a cufflink file like following, with most of the rows have been mapped from XLOC ID to gene symbol, but some of the rows not. Do you know how to map those unmatched ones? Does this mean those unmatched ones are some novel regions without gene name yet? Thanks!

tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length tracking_id XLOC_000005 - - XLOC_000005 XLOC100287934 TSS6 chr1:490755-859671 -
XLOC_000005 XLOC_000006 - - XLOC_000006 - TSS7 chr1:490755-859671 -
XLOC_000006 XLOC_000007 - - XLOC_000007 - TSS8 chr1:490755-859671 -
XLOC_000007 XLOC_000008 - - XLOC_000008 LOC100287934 TSS9 chr1:490755-859671 -
XLOC_000008 XLOC_000009 - - XLOC_000009 - TSS10 chr1:490755-859671 -
XLOC_000009
gene galaxy xloc cufflink cuffdiff • 179 views
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modified 4 months ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by abcxyz5678 • 0
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gravatar for Jennifer Hillman Jackson
4 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, if you used reference annotation and some transcripts were assigned to a known gene/transcript and some were not, those that were not are novel with respect to that annotation source. Check the tracking files for more details (status, etc): Cufflinks manual link

There are several data providers that curate annotation, so you might want to run the analysis using a few different annotation sources (if available for your genome) and compare. Each models the gene bounds/transcripts a bit differently.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k
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