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8.6 years ago
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Hello,
I have transcriptome data. In order to find some species in my data, I plan to blast my sequences . But Is it relevant to blast it against a genome database ? or I need a transcriptome database ??
Cheers
find some speciesas in contamination or exploration of what is present your data? Either database should work since blast will be doing local alignments.Rather exploration of what is present in my data. I want to look for fungi actually. But I'm wondering if it is better to get a genome database or a rRNA database. (I suspect some rRNA contanination in my transcriptome data).
If you want to check every read then blast is going to be very slow but if you want to check a small subset then you could check against nt. Look in http://rnacentral.org/ for specific RNA sequences.
You can try TBLASTX search translated nucleotide databases using a translated nucleotide query. I am not convinced that BLAST is the ideal tool if you are working with short-read sequence data. Is this NGS data and can you provide more details of your task?
What kind of method you think it will be better ? I have RNAseq data from Human, and I want to look if I can find other contaminant species (such as fungus).