Hello all,
I used Tophat to map 100bp, PE Illumina transcriptome reads to a draft genome (133062 contigs).
Our main goal was SNP mining, but I have been suggested the reads could also be used for scaffolding.
I have no experience in genome assembly and scaffolding, but I assume that if I can find read pairs where the 2 reads are mapped to different genomic contigs, the 2 genomic contigs could then be connected.
How can I search the BAM alignments for such read pairs?
Alternatively I could use an assembler that can combine different types of reads such as Mira, but I thought it would take longer, and the genomic reads are not available anyway.
Thank you!
I used Tophat to map 100bp, PE Illumina transcriptome reads to a draft genome (133062 contigs).
Our main goal was SNP mining, but I have been suggested the reads could also be used for scaffolding.
I have no experience in genome assembly and scaffolding, but I assume that if I can find read pairs where the 2 reads are mapped to different genomic contigs, the 2 genomic contigs could then be connected.
How can I search the BAM alignments for such read pairs?
Alternatively I could use an assembler that can combine different types of reads such as Mira, but I thought it would take longer, and the genomic reads are not available anyway.
Thank you!
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