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Hello,
This the first time I am using Cupcake to handle IsoSeq data. I am trying to collapse HQ isoforms from IsoSeq reads (FASTA file) with collapse_isoforms_by_sam.py but it fails. I have already…
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Hi I have run scallop and I obtained a gtf with annotated and unique isoforms reconstructed by scallop. I want to know the gene ID associated to the novel isoform. How can I do this?
thanks for your…
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To annotate this paper PMID:26320947
all process terms
id: GO new1
name: negative masking
Def: The process by which bright light suppresses locomotor activity in a multicellular organism. [PMID:…
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The isokTSP analysis crashes, I think because there is only a single gene in the analysis. Here is the output from R:
`IS analysis of contrast group: rs31.1.u.dark-Col.0.u.dark
Summarising input…
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A significant number of citations were lost from UniProt and RefSeq protein files. Do Medline files need to be downloaded, or is this a processing error?
```
"id_count_diff","id_count_new","id_co…
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Since yesterday I'm preparing the full distribution that was before in a tar at `s3://eu-west-1.releases.bio4j.com/2014_12_03/bio4j_all_plus_isoforms.tar`. Here are the steps performed, just in case w…
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`collapse_isoforms_by_sam.py --input HL60_fltnc_dedup.fasta -s HL60_fltnc_dedup.fasta.sorted.sam -c 0.99 -i 0.95 --gen_mol_count -o HL60_fltnc_dedup.5merge &`
[1] 41376
(SQANTI3.env) [/home/ubuntu/Y…
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Add a column to the table output of `annotate_orf_isoforms` with the Kozak sequence score computed. Likely to use `ORFik::kozakSequenceScore`
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We must improve the way Apollo handles pseudogenes.
Currently, Apollo treats pseudogenes as separate entities with PARENT pseudogene and child transcript, and separate from any other isoforms of the…
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How does one assign an SO term to a variant that lies within the boundaries of one or more transcripts of a gene, but upstream (or downstream) of other transcripts from the same gene?
Consider rs2292…