[dagarfield]

Post the problem anyways. Someone may reply.

[GenoMax]

Hello relipmoc

I am hoping someone is still monitoring this thread--it looks like no one has posted here in about 4 months.

I am having trouble using skewer and I could use some help. I will wait to see if this thread is still active before going into the issue.

Thanks.

As @dagerfiled said please post details about the problem.

Any thread is re-activated once a new post appears. Everyone (who posted in this thread in the past/decided to follow it using thread tools) gets an email when there are new posts in the thread.

[rna_dna]

Hi all

I was able to get the issue figured out before posting my question. I am new to Skewer and it seems SO flexible that there are almost too many parameters to keep track of and to get the right combination of them working to get the right answer is a challenge.

In short, the problem I was having was that I was not using the correct -m setting for what I was trying to do. All I wanted to do was trim the primer sequence from the beginning of some paired-end MiSeq reads. The problem was that I kept trying to use the -m pe since these were paired-end reads. I had tried the -m head, but using just the individual sequence primer fna files, and it only worked for the R1 reads, but would not properly trim the R2s. I was finally able to get what I wanted using -m head, and referencing both the forward and reverse primer sequences as well as both the R1 and R2 together.

% skewer -m head -f solexa -x SM_V4_forward.fna -y SM_V4_reverse.fna Sample_R1_filtered.fastq Sample_R2_filtered.fastq -o Sample_filtered

That gave me the trimmed R1 and the trimmed R2 sequences.

Thanks again for your offers to help.