Challenge 7 - Tweak Filtered FASTQ list?

[zoiediana]

Hi there.

I'm confused at how to address this set of directions from the below paragraph.

"There are a few samples that have very few reads to start with and no reads after filtering. If a sample doesn't have any reads after filtering, filterAndTrim doesn't bother to make an empty filtered FASTQ. We need to manage this, because downstream steps will give us an error if we give them a list of filtered FASTQ filenames that contains names of files that don't actually exist. We need to regenerate our list of filtered FASTQs based on the filtered FASTQ files that are actually present in the directory. We also need to regenerate sample.names from the list of filtered FASTQ files."

I believe it should go something like this: "filt.out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, fnFs=0, fnRs=0" but am not sure.

[zoiediana]

Oh wait it looks like this does it:

filtFs = filtFs[file_exists(filtFs)] filtRs = filtRs[file_exists(filtRs)]

[granek]

Seems like you figured it out. Let me know if you have more questions about this.