Hi everyone, I am currently analyzing RNASeq data obtained from dog cell culture. I used HISAT2 for the alignment to the canis familiaris reference genome in Galaxy. Then, to count the reads, I tried both htseq-count (Galaxy Version 0.9.1) and featureCounts (Galaxy Version 1.6.4+galaxy1). As gene a…

Hi @HanMue The iGenomes version of the annotation is based on RefSeq from several years ago. Annotation from Ensembl will be more current but will require some manipulations to have the chromosome identifiers match up with the built-in canFam3 indexes that are sourced from UCSC. Or, you can also …

Very few genes in htseqCount-/FeatureCounts-Output

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A post was split to a new topic: Reference annotation for TAIR10

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I was trying to count the number of reads through HTSeq but failed.	1	437	January 7, 2019
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Featurecounts in built genome giving no read assignments mapping , transcriptomics , featurecounts	3	469	February 16, 2023
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Very few genes in htseqCount-/FeatureCounts-Output

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