Any way to align a single cDNA sequence against the raw nanopore data?

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#1

Hi, I am trying to check if my interested target gene (GenBank cDNA entry) exists in the raw nanpore sequencing data. I have tried to use minimap2 to compare one cDNA against the fastq format raw data and returned with some .paf file with just numbers like the following pic.

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Is there any method that I could see the direct alignments of the query against the targets, and looks something like this?

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NCBI blast has a size limitation for 10Mb and each of my raw reads fastaq file is over 100Mb.

Or simply, how to examine if my raw sequencing data includes my interested gene?

Thanks!

#2

One thing is not clear to me, did you used blast on galaxy or the webblast of ncbi? With your question BLAST would be the first thing that comes to my mind. Another method would be to first use minimap2 and extract the region of interest based on the start and stop position. After that you could use any aligner you want. But back to blast first, you can create your own blast database with the tool NCBI BLAST+ makeblastdb and you could use this database with NCBI BLAST+ blastn.

#3

Yes, I was confused about the minimap2 results. Because although I see the 10th or 11th column of the result file shows the length of the matched base length, I could not trace back which raw read file it refer to. Second, I have used NCBI blast to do the search then it has a 10Mb limitation. I may try to look into the BLAST+ makeblastdb.