Hi everyone, I'm Carolina (a Master student) and this is my 1st time working with qiime2 in a real case.
I did the tutorials and all the examples that I found in the web and theire was so usefull, but I have a problem with my sequences.
I'm working with the bowel content from rats and send my DNA extraction for 16S rRNA gene amplicon data for do a Taxonomic classification, as the tutorial. The problem is that when the results from sequencing come, there are diferent folders:
- fastq folder: containing all samples already demultiplexed as they come out of the sequencer without any additional quality filtering and trimming applied.
- You will find two files R1 and R2 respectively for each sample. These files contain forward and reverse reads for each sequence.
- cleaned folder: For each sample you will find trimmed and cleaned reads according to the parameters described in the Methods section. When a sequence does not fit the minimum standards of length and/or quality, it is removed from the dataset.
- stats folder: by-samples stats txt files and figures
- joined folder: merged R1 and R2 reads after passing QC (sample.extendedFrags.fastq.gz); notCombined reads are also reported.
- reports: interactive by-semples html files for deeper knowledge on sequencing quality.
- QCReport_LEA22-070.html: This report.
- LEA22-070.md5sum: a MD5sum files to check the integrity of the sequences. In case of a problem while downloading or reading the files, you can check the integrity of the downloaded file by running the following command:
I had worked the fastq folder without problems, because for the import is CASAVA 1.8 and the comand is clear, but I need to work with the joined folder (the marked one) and I've never seen that format before (sample.extendedFrags.fastq.gz) to import to qiime, ¿How can I work with this format?
Thanks for your atention, Carolina.