Problem with FASTA headers and Trinity

Question

[User 4014]

Hi all,

I have a problem with header formats. Since Trinity needs all of the headers to be stitched together, I have some with whitespaces in - that look like this:

@A00700:80:HHHNGDRXX:1:2101:30481:11663#GTGCACCAGGAATCAC 0:N: 00 /1

Can anyone help me with some tips on how to fix these with a bash script or something?

Thank you very much in advance.

[GenoMax]

That looks like a hybrid of old and new Illumina fastq headers. How did you end up with those?

[User 4014]

Actually it is from NovaSeq. The original headers end at #GTGCACCAGGAATCAC, but I guess the 0:N: 00 is added by STAR and /1 is by reformat.sh.

[GenoMax]

Neither makes sense. Can you tell us what you used reformat.sh for?

[User 4014]

Yes, I used it to add /1 and /2 flags. I have mixed RNA-Seq data, but somehow I managed to remove the flags during rRNA clean-up (with both bowtie2 and bbduk) and binning to separate mixed reads from a plant and a fungus (with STAR). Do you have a suggestion?

Answer 1

[ATpoint]

How to remove space in headers of fasta files

[User 4014]

Thanks for the link!