Hi,
My sam file had been sorted by read names using 'samtools sort -n'. Then I used htseq-count to count reads in this sam file; I also double checked by counting unique read names using awk/uniq/wc. The sum of htseq-count output is larger than the number of unique read names. How can this happen? htseq-count count some reads multiple times? Thanks for any hints!
My sam file had been sorted by read names using 'samtools sort -n'. Then I used htseq-count to count reads in this sam file; I also double checked by counting unique read names using awk/uniq/wc. The sum of htseq-count output is larger than the number of unique read names. How can this happen? htseq-count count some reads multiple times? Thanks for any hints!
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