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What are the differences between modes for the --secondary-alignments flag for htseq-count? I had trouble finding the meaning of `score` mode vs `ignore`. Thanks for your help!
racng updated
1 month ago
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Thank you for this tool.
I am a novice in all TCGA data, but I am looking to do some analysis, and I wanted to download TPM normalised values, so that I can compine my own RNA-seq data. I think for m…
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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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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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- `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 @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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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…
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When one or more BAM check fails within the group, htseq-count of the entire group fails. Any way to implement an option so that one can htseq-count on the remaining passing BAMs in the group?