Question: using BBmap to map paire end reads to de-novo assembled transcriptome
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gravatar for rahmati.razieh83
2.6 years ago by
rahmati.razieh8330 wrote:

Dear all

I received some RNA seq reads containing Lexogen primers. My reads do not have any refrence genome. Because of existing primers in the reads, mapping my reads by TopHat to assembled transcriptome will reduce the mapping rate significantly. Regarding having no reference genome, Can I map my reads by BBmap to assembled transcriptome provided by Trinity? Dose BBmap need to reference genome for mapping?

rna-seq • 1.0k views
ADD COMMENTlink modified 2.6 years ago by genomax85k • written 2.6 years ago by rahmati.razieh8330
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gravatar for genomax
2.6 years ago by
genomax85k
United States
genomax85k wrote:

If you are going to align then you will need a reference no matter what genome you are working with. You can use trinity assembled transcriptome as a reference with BBMap. There are other aligners like GMAP that may be useful for this as well.

ADD COMMENTlink written 2.6 years ago by genomax85k

Thank you so much for your comment

ADD REPLYlink written 2.6 years ago by rahmati.razieh8330
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