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DimmestP / nextflow_paired_reads_pipeline

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Bedtools intersect and feature counts give different reads #3

Open DimmestP opened 2 years ago

DimmestP commented 2 years ago

Counts the reads mapped to constructs of interest between the two methods can differ up to 500 reads. Partially because intersect currently does not account for multimapped reads but mostly because they have different regions?

DimmestP commented 2 years ago

Bedtools intersect also gives read 2's mapped to the reverse strand. Should I remove them?