Hi! I am attempting to perform a htseq-count on a HISAT2 aligned read BAM file containing aligned GFF3 and FASTQ data. I am searching for miRNAs, and am aware that the 'feature type' is going to be 'nc_RNA', but I cannot determine the ID attribute to match this. Under the 'annotations' tab in the GFF3 file, three separate annotations are used, and are structured as follows: ID=Cluster_#;DicerCall=_;MIRNA=_. What should I type into the ID Annotation box when performing htseq-count so that it works? Any advice is appreciated!!
The "ID Attribute" is used by the tool to group together annotation lines. My guess is that in your data the common attribute is "MIRNA".
Help from the tool form:
GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-Seq and Ensembl GTF files, is gene_id. (--idattr)
Thanks, Jen, Galaxy team