Hello!
I'm sorry for the silly question, but it's the my first time managing metatranscriptomic data and I'm still confused. I have Illumina shotgun metatranscriptome from my samples. I used bowtie to map each sample to some reference genomes from NCBI and so I obtained one .sam file for each sample. My question is... how should I proceed now? I mean, what are the next steps? Moreover, how can I evaluate the quality of the mapping?![Confused](https://www.seqanswers.com/core/images/smilies/confused.png)
Thanks!!
I'm sorry for the silly question, but it's the my first time managing metatranscriptomic data and I'm still confused. I have Illumina shotgun metatranscriptome from my samples. I used bowtie to map each sample to some reference genomes from NCBI and so I obtained one .sam file for each sample. My question is... how should I proceed now? I mean, what are the next steps? Moreover, how can I evaluate the quality of the mapping?
![Confused](https://www.seqanswers.com/core/images/smilies/confused.png)
Thanks!!
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