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  • Calculating heterozygote bam2count without gff reference

    Hey everyone,

    I have Illumina mRNA Seq data from crosses of two DH brassica napus lines (called lines 3 and 4 => 4 sets: 3x3, 4x4, 3x4, 4x3)
    I created a de novo assembly of the 3x3 with Illumina (-> fasta file),
    mapped the other 3 crosses vs this reference with bowtie2 (-> sam files),
    did SNP calling with samtools and vcftools (-> vcf files).


    Now I want to analyze the 3x4_vs_3x3 (and 4x3_vs_3x3) mapping to find out if certain code fragments are inherited only maternally/paternally.


    So I know there is a routine out there called heterozygote bam2counts here, but this is designed to work with reference (gff) files.
    So my question is: How can I alter the code to work with my de novo assembly? I understand, that it may work somehow with the use of bedtools and the intersect function.

    I'm still new to seqencing and the adjacent bioinformatics. So if anyone can point me in the right direction, that would be very helpful!

    Thank you for reading,
    Simon
    Last edited by Seqql; 03-02-2015, 06:43 AM.

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