-
Hi Heng,
I use the `-x ava-ont` option in minimap2 to get all-vs-all overlaps of ONT RNA-seq reads.
I also output the matching minimizers’ positions in each read for a matched read-pair.
In…
-
-
Hi,
align_and_estimate_abundance.pl requires, depending upon the parameterization, a sub-command `rsem-calculate-expression`:
```
my $cmd = "rsem-calculate-expression $no_qualities_string "…
-
Hi
I am using sqanti3 with the following parameters :
```
Version 2.0.0
Input all_samples.chained.gff
Annotation OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff
Genome OcoaRS1.PZYT01.fa.…
-
I was trying to run Spritz for isoforms and variants using the most recent Spritz version (0.3.10) on 12 paired end fastq files but the program gives an error in rule setup_transfer_mods. I'm running …
trom2 updated
7 months ago
-
Hi,
I was wondering what the event "-" corresponds to ? It is not described in your manual in Bioconductor.
The major feature event of my data are labelled as "-" and I was curious to know why.
…
-
Suppose we can combine multiple assembly graphs and do comparisons between graph structure, label graphs well, etc. What are some reasons we would want to do this for, you know, biology purposes? (For…
-
In semi-model organisms, NCBI and Ensembl usually provide annotations based on ab initio gene prediction and orthology based evidence. With cheap RNAseq, we can build RNA based gene models using Cuffl…
-
The page https://activedriverdb.org/protein/browse/ has a little too much information and should be compressed. I actually wonder if this type of a view is even necessary given that we have top 100 di…
-
Hi Liz,
Apologies if this is a redundant question - I think #7 might explain the results I'm getting too, but wanted to double check.
I'm chaining together some iso-seq samples, and the counts se…