How to map a file with mulitple olisogos to a reference genome

Question

[dominik.lagler]

Hello everyone;)

I have a file with multiple oligos (223471 x 60 nucleotides) which i want to map to a reference genome to see where exactly DNA strands are expected to be captured and then see the actual coaverage on these regions. The problem is that maybe my coverage numbers are "diluted" by the fact that within the target regions all the repeats have been masked and no coverage is to be expected for the masked regions. I justed wanted to ask if the best way doing this is via BLASTn?

The file with the oligos does not have any header just 223471 rows and in eachr row are 60 nucleotides

[gb]

You want the coverage of the oligo's? In that case you may be better of with mapping tools like BWA or bowtie. This can may help as well: https://www.drive5.com/usearch/manual/cmd_search_oligodb.html. But I do think that which whatever method suits best you need to convert your file with oligos to a fasta format. BLAST would be fine I think but then again you need a fasta format input file.

[dominik.lagler]

Thanks for your advice, i converted the file via "Format Converter" (https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html) into a fasta file. After that i aligned it via "bwa" and plotted it with "samtools coverage". Now i have some really nice histograms