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Old 01-10-2020, 09:08 AM   #3
unionicola
Junior Member
 
Location: Wisconsin

Join Date: Feb 2009
Posts: 4
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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!
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