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change "+" in fastq file. phred_offset error qiime

I have a problem with my some fastq reads:

@1V3F_10526394 M01994:35:000000000-BM49D:1:1106:17684:21227 1:N:0:1 orig_bc=GGAATCTCTATAGCCT new_bc=GGAATCTCTATAGCCT bc_diffs=0
+
CGTACACTCCTGCGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGCGGGATGACGGCCTTCGGGTTGTAAACCGCTTTTGATCGGGAGCAAGCCTTCGGGTGAGTGTACCTTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCCTGTAGTCCC
+
CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGDGGCFGGGGGGGGGDGGGFGGGGGGDGGGGGGGGGGGGGCFG@CFGFGCFFGGGFGGFDFGGDGGGEFCGGCFGGGFGGGGGGDGGGGGFGGGGGGGGGGGDGGGGGGGFGDFFGGGGGGGGGGGGGGGGDECGGF7EEGGGGGFGGGGGGGGGGGGGFCGGGGEEGGGEEGGGGGGGF@CEGGGGGGGGGGGGGGGGGGGGFBGDGGGGFDGGGGGCGDGGGGGFGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGEGGGGGGGGFCGGGGGGDGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGFGGGGGGGGGGGGGGGGGGGGGGCCCCC

The first "+" is a problem. How can I delete it?

N.B. not all the reads have this problem so I cannot delete each second line after symbol "@" as I have already tried..

Solution

  • Maybe you can try to remove all "+" lines and then add a "+" line every 3. It will probably be easier than trying to identify is the "+" is placed properly or not.

    cat file.fastq | sed '/^+$/d' | awk '{print; if (NR%3==2){print "+"}}' > fixed.fastq