How reads are aligned to specific region of chromosome?
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I have done some Illumina next generation sequencing after SureSelect target enrichment, and I want to align my reads to a specific region of the genome using BWA.
My fasta file consist of the specific 3 Mb targeted. If the name in the fasta file is, example >chr7:15000000-18000000, BWA doesn't seem to recognize this as the target interval and assumes the first base is at position one. The alignments are then in the wrong position when I try to import into IGV, and the gene annotations are all incorrect.
Is there a way of getting BWA to recognize the target interval, so alignment will be given the correct genomic position if I just use part of a chromosome as the reference sequence? Or do I need to align my data to an entire chromosome/genome so that the positions are correct?
Any suggestion would be very much appreciated!
Cheers,
Oliver
My fasta file consist of the specific 3 Mb targeted. If the name in the fasta file is, example >chr7:15000000-18000000, BWA doesn't seem to recognize this as the target interval and assumes the first base is at position one. The alignments are then in the wrong position when I try to import into IGV, and the gene annotations are all incorrect.
Is there a way of getting BWA to recognize the target interval, so alignment will be given the correct genomic position if I just use part of a chromosome as the reference sequence? Or do I need to align my data to an entire chromosome/genome so that the positions are correct?
Any suggestion would be very much appreciated!
Cheers,
Oliver
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