Reads count decrease after porechop!

[jnarayan81]

Despite of splitting 1,202 / 1,634,477 reads from the middle, and reads count is less after chopping. Did I do anything wrong ?

porechop -i /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta -t 40 > ONT_choppedNcorrected.fa
...
...

Trimming adapters from read ends
     SQK-NSK007_Y_Top: AATGTACTTCGTTCAGTTACGTATTGCT
  SQK-NSK007_Y_Bottom: GCAATACGTAACTGAACGAAGT
     1D2_part_2_start: CTTCGTTCAGTTACGTATTGCTGGCGTCTGCTT
       1D2_part_2_end: CACCCAAGCAGACGCCAGCAATACGTAACT

1,634,477 / 1,634,477 (100.0%)

1,150,024 / 1,634,477 reads had adapters trimmed from their start (40,250,129 bp removed)
  419,580 / 1,634,477 reads had adapters trimmed from their end (6,338,306 bp removed)


Splitting reads containing middle adapters
1,634,477 / 1,634,477 (100.0%)

1,202 / 1,634,477 reads were split based on middle adapters


Outputting trimmed reads to stdout
Done

➜  MyPassport more ONT_choppedNcorrected.fa| grep ">" | wc -l
1633208
➜  MyPassport more /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta | grep ">" | wc -l
1634477

[edwwlui]

in my case, it is due to min_split_read_size after splitting the middle adapters. by default --min_split_read_size is 1000, after splitting if read length < 1000, then the reads are removed.