I start a work in this field (NGS) and some troubles show up... We'd the sequencing through MiSeq for 16S and ITS and we got 120 fastq files (60 forward and 60 reverse). I tried do the upload of the files to MG Rast server and one of this files can not uploaded 'cause show up an message "19,807 sequences of this file were tested. 1 of them contain invalid characters. The FASTQ file is not in the correct format for processing. 112 of the tested sequences are shorter than the minimum length of 75bp. These reads cannot be processed"
Apparently, this specific file is ok since I've checked through Galaxy software and the reads like normal. Somebody have any idea about this problem... Can I "repair" this file and do the upload to MG Rast.
Thank for all.