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Soheil and Jenny have had issues pulling up lncRNAs - check to make sure these aren't being filtered/removed from the counts. Jenny is using GRCh 38 annotations, so we likely just need to map between…
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In concert with with miRNA/transcription working groups.
- [ ] Terms to describe molecular functions of lncRNAs (see GO ontology tracker)
Review all long non-coding RNAs in D.mel and annotate
- […
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T2T chm13-v1.0 CAT annotations for lincRNAs for ENSG00000223812.8 are fragmented due to genomic deletion. However,
they are not flagged as such.
Also, details claim has a CDS, even though it i…
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Please provide as much information as you can:
* **Suggested term label:**
This is a first stab at this term, open to suggestions:
transcriptional interfering lncRNA activity
* **Definiti…
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Hello,
I was wondering if it is more appropriate to use the v1 standard kallisto index https://github.com/pachterlab/kallisto-transcriptome-indices/releases for bulk RNA seq data compared to an ind…
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- [ ] literature search for compensatory mutations in mouse and human for RRIs
- [ ] find RRIs for lncRNAs to test specific model for ncRNAs
- [ ] look at Benchmark data for examples
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Users have requested the addition of AOT and SOT lncRNAs to the GFF file in order to perform differential expression.
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Hi Yang,
Thank you for this great tool! We are interested in organizing subcellular localization of tens of thousands of lncRNAs. But it seems that submitting to the web version of the tool doesn't …
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QC chapter should include a short paragraph on filtering to retain only protein-coding genes.
This is a useful standard filtering step in most datasets, although in some contexts / depending on the…
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Hi,
I am using StringTie (v2.0.3) to search for novel lncRNA transcripts. After running stringtie on my on individual samples, I use --merge to merge samples into a single gtf (with the ensembl ann…