Thank you for your help.
Previously, I was getting the following output results summary:
Code:
Input: 29978820 reads 2188453860 bases.
KTrimmed: 135110 reads (0.45%) 3873797 bases (0.18%)
Total Removed: 29968470 reads (99.97%) 2188332397 bases (99.99%)
Result: 10350 reads (0.03%) 121463 bases (0.01%)
I'm not sure what I was doing differently, but when I repeated the search this morning using the following command (I need to search and remove multiple 8-mers):
Code:
bbduk.sh in=input.fastq literal=AGTCATGC,ACGTACTG,TGACTGCA,TCGACGAT,CTAGCATG,GACTGTAC ktrim=l k=8 rcomp=f outm=removed.fastq out=trimmed.fastq
It gave me the following results:
Code:
Input: 29978820 reads 2188453860 bases.
KTrimmed: 135110 reads (0.45%) 3873797 bases (0.18%)
Total Removed: 9706 reads (0.03%) 3873797 bases (0.18%)
Result: 29969114 reads (99.97%) 2184580063 bases (99.82%)
When I look in removed.fastq, I only see the left most of the reads (from the indicated 8-mer). So it looks like it is working now, but I'm confused as to why/how.
Nonetheless, at least I'm getting the results I want! Thanks for your help again!