bioinfonext

reading large file using bigmemory

13

Hi, I am trying to read a large file using bigmemory and I am getting errors as this file's first two columns are non-numeric, so I have deleted the second...

unmapped sam to pair end reads

1

Hi, How I can extract proper pair end read from these sam files samtools view -S -f4 sample.sam > sample.unmapped.sam

Hi all, I am trying to correct batch effect using combat, could you please help if this is the correct approach or do I need to change the code? I...

I am working on plant species transcriptome. Its draft genome is known. We want to identify some new transcripts in genome-guided assembly. I need your help to remove overlapping sequencing...

remove mitochondria and chloroplast taxa

4

In my phyloseq object, chloroplast is present as class whereas mitochondria present as family: is it correct taxonomy in phyloseq object? > ntaxa(physeq) [1] 67405 > physeq0 ntaxa(physeq0) [1] 66946...

NMDS plot for 16s amplicon

5

I am trying to plot NMDS plot from microbiome data in phyloseq and I used below command, It is working perfectly, but here I used raw otu count for NMDS...

I have done beta diversity analysis using phyloseq PCoA on rarefying OTU data with bray distance and now for statistical significance, I want to use adonis function from vegan so...