counting reads for genes
Hello, I am counting number of reads assigned to each transcript using htseq-count after aligning antennae rna-seq to the annotated tsetse transcripts with STAR but all counts are zero and reads are specified as without features and alignment not unique .can someone help..
here is my command
htseq-count -m union -f bam -r pos -o sam --stranded=yes -t exon -i gene_id /home/billiah/Documents/Projects/responses_of_G.m.morsitans_to_odors/Star_Mapping_Results/Control_Rep_1_output_pairedAligned.sortedByCoord.out.bam /home/billiah/Documents/data_sets/Transctipts/glossina-morsitans-yalebasefeaturesgmory1.9.gtf > /home/billiah/Documents/Projects/responses_of_G.m.morsitans_to_odors/htseq_results/Star_htseq_results/Control_Rep_1_output_paired.counts.bam
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kemuntobilia •
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a common cause for these kind of issues is that the gff/gtf file does not use the same sequence names as in your star index for mapping (or the fasta file or such). Can you check that first?
(so make sure that the sequence names are consistent over all files you are using)