-
For gene-body internal last exons currently the uniquely-exonic regions for each last exon are passed as regions for Salmon to quantify. e.g. for a bleedthrough event, the annotated internal exon is s…
-
Hello,
I'm trying to use STARsolo to count genes and SJ from 10X 3' scRNA data and then I want to use RSEM for isoform quantification. Currently, I'm using STAR v2.7.10b.
First, I generated a re…
-
The traceback:
```
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
FileNotFoundError: [Errno 2] No such file or directory: '/home/rstudio/workspace//data/SspArc0008_10x_c…
-
Dear Brian,
I have a question related to the usage of trimmomatic parameter when performing denovo transcriptome assembly. Upon the usage of the trimmomatic function, it provides the following outp…
-
I am trying the multisample mode, and running into out of memory issues which I expected to occur, but I can only assign a certain amount of RAM on my cluster. Is there a work-around for this.
So …
-
Hi Geo,
I have nanopore cDNA data aligned with minimap2 (with --cs --MD). I tried abundance estimation with StringTie v1.3.5 that should recognize the "CS" tag as an alternative to "XS". The splice…
-
Hi,
can we define Directory in workflow input section? I met error "Cannot coerce expression of type 'String' to 'Directory'".
my wdl file, cromwell 59 is used:
```
version development
workfl…
-
-
### Description of feature
By default, Salmon will drop transcripts with identical sequence, as described here: https://github.com/COMBINE-lab/salmon/issues/214#issuecomment-381580235
This behav…
-
Hey,
First of all thanks for this new implementation of the kallisto software with the D-reference you included in your recent paper *"Accurate quantification of single-nucleus and single-cell RNA-…