Retrieving only Trinity contigs that have mapped reads

[garlic]

Hi,

I am working on the transcriptome of a protist that feeds on another protist (unfortunately, a rather close evolutionary cousin). I have a transcriptome of my target organism mixed with the prey, along with a transcriptome of the prey alone.

As one of the steps in decontaminating my dataset, I am mapping reads from my prey RNA-seq dataset to the assembly of my target organism + prey. I have already taken some other measures to decontaminate the dataset, so I'm not expecting a huge number of my contigs to have prey reads mapped to them.

Does anyone know how (perhaps with SAMtools) I can retrieve only those contigs in my target transcriptome that have prey-only reads mapping to them, along with some metric of how many reads are mapping?

Thanks for your help!

[westerman]

Perhaps I am missing something here but if (a) you have a mapping and (b) know which reads are from prey-only then you should be to -- via samtools view, cut, grep, sort, uniq and the rest of the Linux tools -- generate a count of prey-only, prey+target, target-only for each transcript.

I am not sure if SAMtools per se would help.