Hello Nancy,
The attribute sounds as if it is the correct place in the reference
annotation file (the 9th field), but perhaps there are other
format/content problems with the file. Do you have a tss_id? Do you have
exons labeled?
This is the area of the manual that covers the formatting and
Hi Jennifer,
I did see tss_id in my results and also exon labels. The tss_id was
assigned during the calculation, having the numbers tss1, tss2, etc. By
saying writing codes I mean such as in the link you sent to me, there is:
*Note: *If an arbitrary GTF/GFF3 file is used as input (instead of
Hi Nancy,
It is not quite clear in which steps you used the reference annotation
or how these attributes were lost exactly. Cuffcompare is a tool in
Galaxy - but before we go any further I think that examining the history
would be the speedest path to a solution. Would you share a history
Hi all,
I've been trying to use the cufflinks-cuffmerge-cuffdiff flow to analyze my
RNAseq data. However, cuffmerge lost my p_id. My p_id was originally from
changing the protein_id to p_id by myself in the gtf file. The current p_id
showed up in the same attributes column as gene_id in the gtf
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