We have got a assembled transcripts and raw sequencing data (transcriptome) of an insect from a company we have hired to do the job. and now I wanna know states of how much percentage of the treated insect reads and control group's reads participate in the assembly respectively, or the states of these two group's sequenced reads aligning to the assembled sequences. how could I get these statistical information? Please give me some suggestions!
The reason we do this is the raw data(reads) the company sent to us before could not align the the assembled sequences properly, then we asked them to send us our insect's actual sequencing reads. Then they sent us another set of data one, now we wanna check those reads here. How can we do that?
You need to align the reads back to the assembly using bowtie or bwa. You may get many multi mapped reads as there will be multiple transcripts per gene.