Question: using BBmap to map paire end reads to de-novo assembled transcriptome
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gravatar for rahmati.razieh83
16 months ago by
rahmati.razieh8320 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 • 641 views
ADD COMMENTlink modified 16 months ago by genomax63k • written 16 months ago by rahmati.razieh8320
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gravatar for genomax
16 months ago by
genomax63k
United States
genomax63k 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 16 months ago by genomax63k

Thank you so much for your comment

ADD REPLYlink written 16 months ago by rahmati.razieh8320
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