-
Hello,
This is a very helpful tool for processing htseq count data, and I am using it to get the TPM for some RNAseq counts after running htseq. However, I am not sure how the average read length a…
-
hi,
I have executed the DCC, the circular RNA counts and co-ordinates files are generated. For finding the CircSkipJunction I got the error mentioned below. Can you please guide me resolve this
…
-
Dear all,
I have downloaded HTSeq-Counts harmonized data for Lung Adenocarcinoma.
Raw counts look like this:
```
TCGA-44-7671-01A-11R-2066-07 TCGA-49-6744-11A-01R-1858-07 TCGA-0…
-
Hello
Thank you very much for your work.
I'm trying to run the pipeline using the following code :
st_pipeline_run.py
--output-folder $OUTPUT
--ids $ID
--ref-map $MAP
--ref-annotation $ANN
-…
-
Hello! Thank you so much for including all the code for reproducing analysis! I wanted to ask about treating the strandedness for Smart-seq3 and VASA-seq (plate). Were these treated as unstranded for …
-
macOSX - Sierra 10.12.6
* I downloaded the SPARTA workflow and moved it to the desktop, it did not need to be unzipped FYI.
* typed in the CLI ``` python SPARTA.py```
* Output:
```
Welcome to SPA…
-
I want to download all the clinical data from the rnaseq data selected:
```
expands = c("diagnoses","annotations",
"demographic","exposures")
clinResults = cases() %>%
Genomic…
-
Using voom in the RNA Analysis - Differential Counts tool.
It seems to have worked (there is a table of genes and DGE stats) but the html output file says:
Differential log output
Attaching packag…
-
Hello,
I noticed that gene_quanti seems to be using a strangely high amount of memory.
The command I'm running is: `reademption gene_quanti -p 4 --features 'gene,cds,region,exon' --project_path …
-
Hi,
When I try to run MOP2 with "genome" as the reference type instead of "transcriptome" it doesn't create results. But it seems to be running (with the reference genome I provide) using "transcript…