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Question: see reads in .bam file, no counts after HTseq
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Hi! VERY, VERY (so please be nice to me!) new to the field here, but briefly: performed RNAseq (mouse tissue), got the sequences (fastq format), cleaned them up (trimgalore), aligned them (RNASTAR to mm10) - checked alignments on IGV and can see sufficient reads across all exons for GOI, however when I use HTseq to make count files, GOI has no counts? I've been going through forum after forum trying to figure out where something went wrong, but can't figure it out - any suggestions/insights for investigation into this issue?

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Please provide more detail:

  • copy / paste here the commands you used
  • genome and annotation versions were from same source and version?
  • could you provide a link to the GOI gene?

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