Open MolyWang opened 8 months ago
Hello Zhuyi,
Metagene2 cannot directly produce the plot you need. However, you can use it in rna-seq mode to summarize reads for the 5'UTR, CDS and 3'UTR regions separately, then use the generated tables to produce a combined plot like the one you showed.
Hope this helps, -Eric
Then which intermediate results should I save/output to make the pipeline most straightforward for me? Thanks.
Sorry for the delay!
You need to use the results from the add_metadata or the calculate_ci functions to get the data-frames which will allow you to combine the three types of regions into a single plot.
Cheers, -Eric
Hello Eric, thanks in advance for any help that would be offered!
The data I have:
dm6_tx = GenomicFeatures::transcripts(TxDb.Dmelanogaster.UCSC.dm6.ensGene)
The problem I want to solve: With the above data, I want to produce a metagene plot to summarize where the sequencing reads come from, whether they are 5'UTR, CDS, or 3'UTR. (In this case, I would like to collapse the whole genome into one generic transcript schematic. The x-axis of the output plot would be a generic transcript, and below would be something similar to my expected plot.)
One final question: Now isoforms would matter in my case, because different isoforms of the same gene may have different TSS and TES. If necessary, I have data to select the most abundant isoform for each gene, but is there any way to produce the plot without this selection?
Thank you again, Zhuyi