Hi Jen:
I still have a little problem with the chromosome names. It appears that the
mitochondria genes and chloroplast genes are named ChrC and ChrM in the
gff3 file which I need to change to chrC and chrM. How do I change cases
specifically for the initial letters and not the entire words?
Hi Yang,
I am going to give you a method to do this - in short you'll be
splitting the dataset into three parts, altering two of them, then
merging the three final results datasets together. A workflow could be
extracted from the history once you have completed this method, saved
for future
Hello,
It looks like the data is mapping as novel - not linked with the
reference annotation. There can be a few factors that can cause this to
occur for part of a dataset (often desirable) but when it occurs for an
entire dataset, there is often a data mismatch or parameter issue.
The
Hi Jen:
Thank you for the prompt reply. RPKMs produced by cufflink look normal (from an
assembled transcript file):
Seqname Source Feature Start End Score Strand Frame Attributes
chr1Cufflinks transcript 11960 13178 1000. .
gene_id CUFF.180;
Hello Yang,
Glad the problem was isolated - the mismatched chromosomes is definitely
something to be fixed.
The tools in 'Text Manipulation can help. The tool Change Case of
selected columns can change the case for you. Click on the pencil icon
after running the tool to reassign the
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