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What Are Recommend Approaches For Studying Bacterial Rna-Seq Data

I have a data from Hi-seq for a bacterial RNA-seq , however, it is an over kill, with any aligner it gives ma around >1GB data no mismatch. What may be the best strategy to analyze such data? I think if I take a fraction of the data that may be useful but I dont know how I can take fraction of aligned reads from Bam file? Any suggestion please?

rna-seq bacteria
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updated by Istvan Albert Istvan Albert • written by Honey Honey

Sorry, I don't understand the question. Can you clarify what you mean by "around >1GB data no mismatch"?

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written by Mikael Huss Mikael Huss

1 answer

sample was contaminated?

blast with unmatched reads to see where may these come from

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written by luwening • luwening

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