samtools to count the number of reads mapped to each spike-in for each sample

samtools to count the number of reads mapped to each spike-in for each sample

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My goal is to use STAR to create a new genome with the spike-ins listed below by combining both hg38.fa and spike-in. Once I have the genomes created, I’ll align FASTQs to this newly created genome and use samtools (or another tool) to count the number of reads mapped to each spike-in for each sample. Would anyone know how to use samtools in this case?

Spike-in 150bp:

AGGCTTTGTTATTGGTATTGACTTACAAACAGTTAAGCCATTTGAATATGATAATGTAGTTGCAATAAAAGGAGATTTCACCTTAGAAGAAAATTTGAACAAAATTAGAGAGCTAATTCCAAATGATGAAAAAAAGGTGGATGTGGTTAT

Spike-in 250 bp:

ACGATAAAATTGGTTTTGCCTTTCAGCAATTCAACTTAATTCCTTTATTAACTGCCTTAGAAAATGTTGAACTTCCACTGATTTTTAAATATAGGGGAGCAATGAGCGGAGAAGAGAGGAGGAAGAGAGCTTTAGAATGCTTAAAGATGGCAGAGTTGGAGGAGAGATTTGCCAATCACAAACCAAATCAGTTGAGTGGAGGGCAACAACAGAGAGTTGCTATAGCGAGGGCTTTGGCAAACAACCCACC

Spike-in 350 bp:

CACCTGTCACATTTCCAATCGGCTCCAGGAAGAGAGAAGTGACGGCTTGATCCTGTAGTAATCCGGGATCGACTTAAGGGGTGCAGCGACCACGGCGGATCGGGCGTCGCAATAGTCCTCCTGTTAGGAGGGTCCTTCTAATGTTAACGCCCGAATATTAGTCATATTTTGCTAGCGCCTATCAGCGTAAGATATGATTTAAGTTACACCAGGAGAGTAGCGAGATAGAACCACTCGTTGGATCGGTCTTTCTTAATTGACTACTATCAGATCCGGCGCATGGCGCTGAGGTCAAACTACATTACAGGCCCTGGTTTCCATGGGTCAGCGCAAGTACAGGCGAGCAGATA

Spike-in 450 bp:

CACAAGAATCCCTGCTAGCTGAAGGAGGGTCAAACTATAACACCTTTAGCATTCGTACAGGCAGGCTAAGTGAATACTAACCCACCGGCAGCCCGTTGTAGTAACGTTGACCCCTGGCTCGGAGACATTTGGTGTTGCCTAGTACTAGGTGACTGGTACCGATTCATAGGTTCGCCATTCTCTTATCGAGAGCCCGAGGTAGACTATCTTCCAGATGATGCCATACGTTCACTCAATCGCGCGGCATGCACGGTGGGGCTACGAACTTGCTATCCATAGGCTCTAGATGTGGTAGAAATATGCTGCAGGGGTTCTGTCGAATTTGCTCGGCAACCGTGGCCGTGTATGCTTTCATATCCCGGCGGTGTGATCTAGCCTTCTCGCCATATGAGGGCGCTGAGCATAGACCCAAACCCGACTAGTCGAATCTTAGGGTTGTATGCTAGAACG


alignment


samtools

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