lost contigs along the way ?

[TristanLefebure]

Hi,

I have a trinity assembly that contains 215578 contigs:

[tristan@umr5023-proasellus PCG6_rapclust] grep -c '>' ../trinity_assembly.fa
215758

I ran Salmon, and got expression for these 215578 contigs:

[tristan@umr5023-proasellus PCG6_salmon_transcripts_quant] wc -l quant.sf
215759 quant.sf

But RapClust only returns cluster assigment for 134922 contigs:

[tristan@umr5023-proasellus PCG6_rapclust] wc -l mag.flat.clust
134922 mag.flat.clust

How come?

Thanks!

[laraib85]

Hi,

RapClust removes contigs that have less than 10 reads mapping to them. That's why the drop in total contig count.

[TristanLefebure]

thanks for the info !