I am new in this field. I am doing metagenome analysis with shotgun reads. All reads are single ended. DNAs were obtained from airways of human. I just want to find taxon abundances in the samples. Then I will predict the diversities and core microbes.
My mapping results are terrible. How can I handle bad mappings?? OR should I change the tools that I used the analysis?? Which tools are more accurate or sensitive for microbiome analysis?? I need any suggestions, please!
I followed this pipeline:
- Assembly was done using Megahit
- Short contigs (<200 bps) were removed using prinseq
- Read mapping against contigs was performed using BWA
- Similarity searches for GenBank, KEGG, eggNOG were done using Diamond
- Binning was done using MaxBin2
This is my mapping results:
# Sample Total reads Mapped reads Mapping perc Total bases samples13 21380728 17881628 83.63 1618006383 samples14 109599 22051 20.12 7606328 samples15 258752 119090 46.02 18803788 samples16 340586 147490 43.30 24935657 samples12 7342679 6205921 84.52 524794709 samples11 7741157 6283578 81.17 554721680 samples17 17108901 15213361 88.92 1294292384 samples18 4012626 2850684 71.04 302834087