-
### Ask away!
Hi, I'm trying to specify the minimap2 parameter '--junc_bed' with a bed file of splice annotations to ensure the correct splice sites are mapped around my gene of interest, which is so…
-
When having a deletion that spans from before a splice site to after a splice site, Funcotator does not properly render Codon Change or Protein Change.
For frame shifts, this is because Funcotator …
-
I ran STAR ALIGNER 2 pass_mode with default parameters and got 3899739 splice junctions in Log.final.out file whereas there are only 179k splice sites in SJ.out.tab file. I wanted to know wether this …
-
"Make Intron" is supposed to take as a starting point the genome coord clicked on in an exon, then search around that point for the closest canonical splice sites, and effectively create an intron by …
-
Hi,
I am trying to run rmats in the HPC. I installed rmats in a new rmats environment in conda.
I activated conda and the environment, but somehow I just can't run it. I got several errors.
I f…
-
Hi! I had this issue:
```
time VirID assembly_and_basic_annotation -i SRR1007830
5_1.fastq -i2 SRR10078305_2.fastq -out_dir virid_output --threads 24
[2024-10-01 11:41:45] INFO: VirID v3.1.0
[…
-
Hello, I'm sorry if this is rather elementary.
But I attempted to generate the appropriate input bam files for uncalled4 align via the following command:
`guppy_basecaller -i /fast5_directory -…
-
Jupyter Server /* disable initial hide */ div#header, div#site { display: block; } Jupyter Server requires JavaScript. Please enable it to proceed. 404 : Not Found You are …
-
Do genomes include...
- splicing during start/stop codons
- alternative splice sites
- any dinucleotide bias at transcription start site
- ...
-
I think the information in the junc-bed file can be better utilized by minimap2 in dealing with cases that deviate from the default settings. Two such cases:
1. When there are non-consensus splice j…