-
Hi @jaudoux
I am wondering how gene-counts.tsv.gz, transcript-counts.tsv.gz are being generated, Are they raw-counts, or using a feature counting tool?
In my opinion, it would be so handy if the…
-
The pipeline seems to be working, but I don't get the same output.
I used the sMETASeq_NEXTFlex.sh for D12_S12_R1.fastq file only (due to limited space on my laptop). My commands look like this (I…
-
Hello
I'm use R 3.5.1. I got the GDC data-molecular data-hamornized database(hg38)-Project KIRC-Transcriptome Profiling-Gene Expression Quanlification-HTSeq FPKM UQ-Primary solid tumor and download s…
-
An output format that contains counts for all transcripts (in standard order) would be useful for downstream analysis. Like most other quant software (htseq-count, kallisto, salmon)
-
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…
-
**Software versions**
- `HTSeq` 2.0.1
- `Python` 3.9.2
- operating system Ubuntu 18.04
**Describe the bug**
I was trying to use the in operator to determine whether any values were set in a spe…
-
Hi!
I'm doing a project to do Differential gene expression on non-coding RNAs, so was planning to filter counts file only for non-coding probability.
But for that to happen, I'd need the read i…
idlip updated
3 months ago
-
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,
I performed below command. Why counts of rows of "fpkm_matrix" inconsistent with that of "counts"?
================
library(countToFPKM)
counts
-
Hi,
I'm trying to count single end reads aligned to a genome with STAR, this command line i'm using:
`htseq-count -f bam ZF_C1F.Aligned.sortedByCoord.out.bam ../Annotation/ZebFish.ncbiRefSeqCura…