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BGI-flexlab / SOAPnuke

A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files
GNU General Public License v3.0
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number of filted reads is wrong #30

Closed lituan closed 5 years ago

lituan commented 6 years ago

following is output in Statistics_of_Filtered_Reads.txt

the number of "Read with n rate exceed: (%)" is wrong, 4450 != 477 + 2079

Item Total Percentage Counts(fq1) Percentage Counts(fq2) Percentage Total filtered reads (%) 6788 100.00% 3394 100.00% 3394 100.00% Reads with adapter (%) 2316 34.12% 1155 34.03% 1110 32.70% Reads with low quality (%) 22 0.32% 2 0.06% 9 0.27% Reads with low mean quality (%) 0 0.00% 0 0.00% 0 0.00% Reads with duplications (%) 0 0.00% 0 0.00% 0 0.00% Read with n rate exceed: (%) 4450 65.56% 477 14.05% 2079 61.26% Read with small insert size: (%) 0 0.00% 0 0.00% 0 0.00% Reads with PolyA (%) 0 0.00% 0 0.00% 0 0.00%

youngchan919 commented 5 years ago

4450 <= (477 + 2079) * 2 the stats contain the overlapped counts