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revise doc for overlap detection
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sfchen committed Apr 17, 2019
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# base correction for PE data
`fastp` perform `overlap analysis` for PE data, which try to find an overlap of each pair of reads. If an proper overlap is found, it can correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality. If a base is corrected, the quality of its paired base will be assigned to it so that they will share the same quality.  

This function is not enabled by default, specify `-c` or `--correction` to enable it. This function is based on overlapping detection, which has adjustable parameters `overlap_len_require (default 30)`, `overlap_diff_limit (default 5)` and `overlap_diff_limit_percent (default 20%)`.
This function is not enabled by default, specify `-c` or `--correction` to enable it. This function is based on overlapping detection, which has adjustable parameters `overlap_len_require (default 30)`, `overlap_diff_limit (default 5)` and `overlap_diff_limit_percent (default 20%)`. Please note that the reads should meet these three conditions simultaneously.

# global trimming
`fastp` supports global trimming, which means trim all reads in the front or the tail. This function is useful since sometimes you want to drop some cycles of a sequencing run.
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@NB551106:9:H5Y5GBGX2:1:22306:18653:13119 1:N:0:GATCAG merged_150_15`
means that 150bp are from read1, and 15bp are from read2. `fastp` prefers the bases in read1 since they usually have higher quality than read2.

Same as the [base correction feature](#base-correction-for-pe-data), this function is also based on overlapping detection, which has adjustable parameters `overlap_len_require (default 30)`, `overlap_diff_limit (default 5)` and `overlap_diff_limit_percent (default 20%)`.
Same as the [base correction feature](#base-correction-for-pe-data), this function is also based on overlapping detection, which has adjustable parameters `overlap_len_require (default 30)`, `overlap_diff_limit (default 5)` and `overlap_diff_limit_percent (default 20%)`. Please note that the reads should meet these three conditions simultaneously.

# all options
```shell
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