chrissy005

Hello, I am trying to filter out genera that have relative abundances less than 10% after collapsing the ASVs into Genus using tax_glom. I am attempting to do this as...

Error in method = cicrlize with plot_sum_links

8

Dear Chi Liu, I am getting an error when using this code for plot_sum_links for my data ( t1$plot_sum_links(method = "circlize", transparency = 0.2, annotationTrackHeight = circlize::mm_h(c(5, 5)))) My exact...

Convert net_construct or net_analyse object to trans_network or cal_network class

16

Dear @ChiLiubio, I have already constructed my network plot using NetCoMi with measure as 'spieceasi' and I was wondering if it is possible to import the net_construct or net_analyse object...

Hello, I am using bowtie2 for the first time to remove human-associated sequences from my set of environmental sequences. However I am not certain on which build I should download...

I have managed to create a heatmap such that each slice has a different color using 'layer_fun" as follows: col_fun_C1 = colorRamp2(c(0, 1606), c("white", "cadetblue")) col_fun_C1_methane = colorRamp2(c(0, 487), c("white",...

Can MAGs in .gbk format be used as input files to the pipeline for eggNOG annotations?

Filtering host reads

1

Hello, I was attempting the following codes as you described to filter out host sequences:. "host sequences: mkdir host not_host samtools fastq -F 3588 -f 65 output.bam | gzip -c...