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Greetings.
I have been using Btrim for some time now to trim Illumina reads for quality with great success -- unless I am starting with reads of 75 or 50 (rather than 100).
When I use 75 or 100bp reads, I always get this result:
My basic command that works is:
I have also tried:
In addition, I tried larger window sizes (5 and 10) and I even tried lowering the quality threshold to 20.
I still can't get it to trim my reads, always the same results.
(The ones I am working with now are 75bp)
I have been using Btrim for some time now to trim Illumina reads for quality with great success -- unless I am starting with reads of 75 or 50 (rather than 100).
When I use 75 or 100bp reads, I always get this result:
Code:
Total sequences: 9831943 Pattern trimmed: 0 Qual trimmed: 0 Total passed: 0 Short: 9831943
Code:
Btrim64 -q -t MySeqs.FASTQ -o MySeqs_trimmed.FASTQ -w 1 -a 30
Code:
Btrim64 -q -t MySeqs.FASTQ -o MySeqs_trimmed.FASTQ -w 1 -a 30 -l 10)
I still can't get it to trim my reads, always the same results.
(The ones I am working with now are 75bp)