Can you convert ASCII text to fastq?

Question

[emi-smiley]

Hi smarty pants peeps,

I got sequence files from collaborators and their original file types look like this:

File: MG430_L4_2.fq.gz,  Type: application/x-gzip  File: MG431_L4_1.fq.gz, Type: application/x-gzip  File:MG431_L4_2.fq.gz,  Type: application/x-gzip

I ran fastqc, trimmomatic (removing adapters) and then fastqc again. I then started running Humann3 and was runnning into errors before realizing that the output files from trimmomatic were in the "ASCII" format:

File: MG469_L2.trimmed_2P | Format: ASCII text  File: MG469_L2.trimmed_1P Format: ASCII text 

I think this is the reason Humann isn't working and I'm wondering it you know if I can convert ASCII to fastq format. When I view the originals and then these ASCII as a text file and look at the reads, it all kind looks the same to me. So it's a mystery to me and I'm wondering if anyone has encountered this? Can I convert ASCII text to fastq? Is it something wrong with the way I trimmed my files?

Answer 1

[cfos4698]

It's normal for reads to be ASCII text if they aren't compressed. Your original files from collaborators are gzip compressed, then your trimmed files are not compressed. The documentation for Humann requests the following input types:

Types:

File Type 1 (a quality-controlled metagenome or metatranscriptome)
- fastq (fastq.gz) 
- fasta (fasta.gz)

File Type 2 (alignment results type 1)
- sam
- bam
File Type 3 (alignment results type 2)
- blast-like tsv
File Type 4 (gene table)
- tsv
- biom

So, it's likely that you just need to gzip compress your trimmed reads. You could have had the reads compressed by trimmomatic automatically. However, you can still do it post-hoc using gzip.

Edit: another possibility (I haven't looked further) is that humann accepts either optionally compressed or uncompressed reads, in which case you have a further problem. We won't know unless you show us the commands you gave to both humann and trimmomatic, as well as the exact errors.