I am attempting to align some raw sequencing reads to a set of recently published, universal gene probes. I would like to be able to create a coding script that can be used for future species downstream. My goal is to see which raw reads align with genes from the set and use those for a trial sequencing run. I have recently used Bowtie to align to a genome, but it seems to me that reference sequence programs like Bowtie2 build indices from a whole genome fq file. Does anyone have any suggestions?
Hi Ryan Fuller what do you mean "build indices from a whole genome fq file"? Do you mean reference genome fasta file?
If you don't want the program to build indices for the whole genome sequence file, I would suggest you to extract only the set of genes that you want to map your reads to, and combine them in a multi-fasta file, then use it as reference sequence file to build indices for (e.g., using bowtie2 or BWA). After that, you could map your raw reads against the new reference sequence set.
You can use mega for global allingment. Also there are number of online tools. Please visit to EMBL website
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