make.sra generated the length of the quality reads (in submitted file) is longer than the sequence reads


I really appreciate the make.sra command, which potentially makes my life much easier to submit sequencing data to SRA NCBI. I did run into a problem, however, as SRA sent email saying “Your submission is currently in error because the length of your quality reads is longer than the sequence reads in your files. Possibly this is from removing barcodes/adapters from the sequence and not the qualities? Do you have versions of these files where the sequence and qualities are of equal length?”

I suspect that maybe I didn’t use the right fastq file? The question would be: which fastq file to use for make.sra command, please?

What makes it worse is that this data set is an old one from Mr. DNA. It means the raw fastq files have mixed forward and reverse reads. Also they only tagged barcode at on end. I played around the data set by doing

make.contigs (ffastq=xx_R1.fastq, rfastq=xx.R2.fastq)
trim.seqs( fasta=current, oligos=xx.oligos, checkoriganl=T, maxambig=0, minlength=100, maxlength=500)
make.fastq(fasta=current, qfile=xx.qual)
Then I used the fastq that I generated to run make.sra
Any potential mistake here, please?

And any suggestion for dealing with Mr.DNA data for SRA submission is really appreciated!!


This way works. Just a reference if anyone has similar situation.