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HTseq-count is strand-specific in default. Therefore, read counts for each gene in gene_counts_HTseq.gff are approximately a half counts in gene_counts.gff for the corresponding gene.
Bedtools multicov output format:
Bedtools output file will be a tab-delimited file with all columns of the gtf/gff file (annotation file) followed by a count column for every input sample .
Columns for our output file are the following (the columns newly added by bedtools in bold):
chr/seqname source feature startposition endposition score strand frame attribute C1_R1count C1_R2count C1_R3count C2_R1count C2_R2count C2_R3count
HTSeq output format:
HTSeq output file (after concatenation) will be a tab-delimited file with the feature name followed by a count column or every input sample.
Columns for our output file are the following
Genename C1_R1count C1_R2count C1_R3count C2_R1count C2_R2count C2_R3count
Gene Counting If you Mapped to the Transcriptome
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