Dear community members,
Sorry for this long posting!
I received fastq.gz files from sequencing company and a seperate excel file including the details of sample id, index7, index5 and noheader column as shown below
sample index7 index5
sample-1 CTCTCTAC CGTCTAAT N704-S506
sample-2 GGACTCCT AAGGAGTA N705-S507
when i open the fastq file, these index7 and index5 sequences are seen at the last in the header as shown below
From the sequencing company i learnt that the BCL(base calls) binary is converted into FASTQ using Illumina package bcl2fastq (in which, the barcodes are supposed to be removed), while stating that adapters are not trimmed from the reads.
So now i wonder that, when i look into the fastq files, the header section contains the index7 + index5,
but when i look into sequence, i am unable to distinguish the adapter and primer sequences.
The following where the adapters + primer sequences
V3-F : TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG+CCTACGGGNGGCWGCAG
So,considering that my sequences are without adapters (preprocessed), I tried all the QIIME2 steps including qiime cutadapt trim paired, which resulted in 0 trimed sequences followed by DADA2 deniosing and further steps and ended with 4851 features from 24 soil samples.
So whether, my analysis is right or am I missing any filter process.
Once again sorry for this long posting!
At the same time, when i tried with qiime1 steps like given below ended with 70,380 OTUS.
identify_chimeric_seq.py, filter_fasta.py, pick_open_reference_otus.py using usearch and summary_taxa.py
So i doubt that my preprocessing steps are having faults. I would like know how to preprocess my fatsq files that contains index 7 and index 5 in header section. Also, I would like to know, whether the presence of index7 and index5 in the header is affects my end results.
Though , I´ve been following several tutorials found in forums, but I still don´t understand how to process this data. In addition, I do not know how to get the mapping file because of the structure of the sequences provided.
I would like to receive some help on preprocess these fastq files and to proceed further with QIIME1 and to import into QIIME2.
Thank you in advance!.
Thank you in advance.