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  • Help with sgRNA CRISPR screen mapping to reference genome

    Hello everyone,

    I am relatively new to NGS and bioinformatics and am working on CRISPR screens in cell lines.

    I would like to create a reference genome containing approx 120 000 different sequences. I have a fasta and txt file containing all sgRNA sequences along with the gene they target, like this:

    "Gene" "id" "Sequence"
    "A1BG" "HGLibA_00001" "GTCGCTGAGCTCCGATTCGA"
    "A1BG" "HGLibA_00002" "ACCTGTAGTTGCCGGCGTGC"
    "A1BG" "HGLibA_00003" "CGTCAGCGTCACATTGGCCA"
    "A1CF" "HGLibA_00004" "CGCGCACTGGTCCAGCGCAC"
    "A1CF" "HGLibA_00005" "CCAAGCTATATCCTGTGCGC"
    "A1CF" "HGLibA_00006" "AAGTTGCTTGATTGCATTCT"
    "A2M" "HGLibA_00007" "CGCTTCTTAAATTCTTGGGT"
    ...

    I would like to create a reference genome so that I can map my reads to this file, allowing for one mismatch (BAM alignment?) .

    Thanks a lot,

    Matt

  • #2
    You can use bowtie2-build to build an index for mapping with bowtie2.

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