Hi,
I noticed that the HTSeq-count output does not have any reads unambiguously mapped to pseudogenes and transposons. I havent checked the no-feature and ambiguous reads. I wonder whether HTSeq classifies reads mapping to pseudogenes/transposons as no-feature or as ambiguous? If neither, then what?
I had used the following command-line:
Any suggestions appreciated!
Thanks
Flobpf
I noticed that the HTSeq-count output does not have any reads unambiguously mapped to pseudogenes and transposons. I havent checked the no-feature and ambiguous reads. I wonder whether HTSeq classifies reads mapping to pseudogenes/transposons as no-feature or as ambiguous? If neither, then what?
I had used the following command-line:
Code:
python -m HTSeq.scripts.count -m union -s no -t gene -i ID -o myfile.gff.readcounts accepted_hits.sam myfile.gff
Thanks
Flobpf
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