behavior of fastq-mcf for two adaptor clipping toy examples

[Yiping Zhan]

Hello Erik and experienced EA Utils users,

I'm puzzled by the behavior of fastq-mcf in the following two examples. Could anyone offer insights in case I'm missing anything?

First I prepare a one read fastq file and two different adaptor fasta files.

echo -e "@1\nAATGGGCACGACGGACGACTATATCTACGACTGTTACTACGACT\n+\nhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh" > yyy.fq

echo -e ">1_3p\nAATGGGC" > xxx1.fa

echo -e ">1_3p\nTTTCGTA" > xxx2.fa

Output for the two example commands are shown below.

Example 1:

$ fastq-mcf -o zzz.fq xxx1.fa yyy.fq

Command Line: -o zzz.fq xxx1.fa yyy.fq

Scale used: 2.2

Phred: 64

Threshold used: 1 out of 1

Adapter 1_3p (AATGGGC): counted 0 at the 'end' of 'yyy.fq', clip set to 1

Files: 1

Total reads: 1

Too short after clip: 1

Example 2:

$ fastq-mcf -o zzz.fq xxx2.fa yyy.fq

Command Line: -o zzz.fq xxx2.fa yyy.fq

Scale used: 2.2

Phred: 64

Threshold used: 1 out of 1

No adapters found, no skewing detected, and no trimming needed.

Files: 1

Total reads: 1

Too short after clip: 0

For example 1, I don't understand why the sequence is considered too short after clip since it's longer than 19, the default length cutoff. Clipping is not carried out as expected in this case.

For example 2, I don't understand why the output says "No adapters found". The first example does not behave this way.

Thanks,

Yiping