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Hi Brian,
How can we retain those transcripts if transcripts were not predicted to contain a protein-coding ORF (using blast and pfam), as long as they meet the minimum transcript length?
Also h…
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Hi,
Can't complete the pipeline. I get an error.
```
executor > local (27)
[15/32ba1b] process > fasqc (reads_R) [100%] 1 of 1 ✔
[c5/32f96c] process > fastp (reads_R) …
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Dear Brian,
For my RNAseq experiment, I would like to use the predicted transcripts for the genome of my organism as a transcriptome reference. To do a GO enrichment analysis, I was thinking of an…
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HI,
> If you have RNA-Seq data and have reconstructed transcripts using a method such as [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/) or [PASA](http://pasapipeline.github.io/), you ca…
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Transdecoder by default dumps the final output files into the current directory, regardless of output folder settings.
Should figure out how to change this behavior using TransDecoder or just mv the …
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Hi, there.
Since I have used the stringtie merge parameters to combined all the gtf file together. As we can see that there are just the transcripts and exons features in the final files.
![imag…
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Hi Lars,
My team has recently curated over 20k genes for a novel Caenorhabditis genome we have assembled. I noticed that we underperform in sensitivity relative to TSEBRA annotations (generated by …
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Hi I am writing to consult the reason of an erroneous GFF file checked by "_gff3_gene_prediction_file_validator.pl_".
This GFF file "**isoseq_all_four_tissues.fastq.transcript_models_IDfixed.gff**"…
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Hi, I am getting an error when running sgt_constructor.py on Linux x64.
I can start the run with an M1 mac but with the RAxML problem, it cannot complete correctly. I am also using a larger data set …
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Dear developers,
Thanks for this great tool.
I am using the latest igv.js (v2.12.6) released in 2022.Jun.
I am trying to load one large genome using `igv.js`. One popup box with information l…