Hi all, sorry for this question, i know it might have asked so many times. I just want to get more insights into it. Please provide your inputs. Thanks in advance.
I have sequencing data (2✖300) of V3-V4 regions. This is a look of my fastq files which includes 2 index sequences in the header. Is there any need to remove these sequences.
When i denoised it using these parameters, i found very weird results.
Truncate length of forward: 220
Truncate length of reverse: 190
I selected these length based on quality of reads.
After denoising, i got very few number of features and frequencies.
The stat table is showing i have enough number of reads but not merged and non-chimeric reads. There is a problem with merging of forward and reverse reads. I think forward and reverse read are not overlapping properly. Could you please input your suggestions, what should i do to resolve this issue. What should be the length of forward and reverse read for enough overlapping.