I am finished with my analysis and need to archive my sequences. I am trying to use the make.sra command, but all of my sequences end up in scrap. I am hoping you might be able to help.
Here are some details:
Sequences: MiSeq paired 16s rRNA reads. One forward and one reverse fastq file.
Command: make.sra(file=paired_fastq.file, oligos=barcodes.oligos, project=My.project, mimark=barcodes_mimark.txt, pdiffs=1)
My paired_fastq file looks like: forward_S1_R1.fastq reverse_S1_R2.fastq
My oligos file (same one used for make.contigs) looks like:
Primer ATGCA… TGACG… V3V4
Barcode GTTAC… TCAA… F1R1
…etc
My mimark file (generated using get.mimarkspackage) looks like:
F1R1.V3V4 aquatic metagenome …etc
F1R2.V3V4 aquatic metagenome …etc
…etc
No errors in output
Output File Names:
paired_fasta.scrap.forward.fastq
paired_fasta.scrap.reverse.fastq
paired_fasta.xml