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Hello,
I'm trying to run a script using HTSeq- count. I tried to use **--add-chromosome-info** as I need to have the chromosomal coordinate in my output file. Here is the script that I used:
**m…
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Hi, the version of nbformat present in the yaml to install the conda environment is not present in any of the channels. I have tried to install the newest one but it fails with some inconsistent requi…
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Hello,
I am experiencing the following problem all of a sudden:
"100000 alignment records processed.
200000 alignment records processed.
300000 alignment records processed.
Error occured when…
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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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Hi developer,
Thank you for creating such a fast and helpful software; it's been very useful for my work.
My objective is to remove rRNA reads and retain only those reads that do not contain rRNA…
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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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- `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 …