Fastx_reverse_complement error. Invalid quality score even with -Q33

Question

[roblogan6]

I am using the fastx toolkit to get the reverse complement of fastq files that are in Sanger phred 33 format. I need to add the -Q33 flag, as discussed in this previous BioStars post Fastx Invalid Quality Score Value . However, I am getting the following error:

fastx_reverse_complement: Error: invalid quality score data on line 1464 (quality_tok = "+"

The "+" symbol on this line is a low scoring phred 33 symbol, not the "+" that separates sequence lines from symbol lines. The fastq files were generated from PacBio, which are in Sanger 33 format. I don't know why it is not being recognized or accepted. Any insights on how to overcome this? Thanks

Answer 1

[Brian Bushnell]

Use BBMap's reformat tool:

reformat.sh in=reads.fq out=rcomped.fq rcomp qin=33

That gets used daily with PacBio reads without problems. Fastx is a bit obsolete.

[roblogan6]

Thanks Brian for pointing me in the right direction. BBMap worked very well. I noticed you are the author of BBMap too. Very cool! Thanks again.

[Brian Bushnell]

You're welcome, glad I could help!