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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 …
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Hi, I'm trying to install scPathoQuant in my server. I used conda virtual environment with python version 3.12.2 and follow the instruction. But the error log indicates that the python version is too …
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Some tool choices in RNAseq are a matter preference, in that the evidence is not clear enough to enable an empirically or theoretically motivated choice. However, some things are just demonstrably bad…
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Hi @zhxiaokang
i run into a problem when i execute the pipeline with the paired-end test data using htseq-count. There appears the following warning and finally the Error caused by missing file:
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I found several ways to calculate the FPKM-uq, and non of them performed well in the predictions.
Can you clarify the formal way to calculate FPKM-UQ from counts matrix?
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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…
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- `HTSeq` 2.0.5
- Python 3.10.13
Hi,
I am trying to parse the canonical transcripts from the ensembl reference annotation with the GFF_Reader. For this I need to use the 'tag' attribute. There …
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Hi developer,
I am using SortMeRNA to remove rRNA from my metatranscriptome data, and while I expected most rRNA reads to be depleted. The cleaned reads contain 25,721,937 R1 and 25,721,937 R2 reads…
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Picard and HTseq are still in a conda environment that must be activated when starting the script
We have found no docker images with functional Picard
For HTseq, we should create a docker image c…