cDNA database based on genome resequencing



I have some expression data acquired with old microarrays.
The microarrays has been designed using ESTs from several maize lines, non-traceable.

Now, I have data from transcriptome profiling using these microarrays but for other maize line.
The reference genome is B73 and I think most of probes has been done for it, though I can't prove it.

The natural thing would be mapping oligo probes to the B73 genome to see how the probes relate to new data on its sequence.

The problem is that I have done experiments with material from other line. So maybe it would be better to map oligos to transcripts of "my" line.

I have the genome of "my" line resequenced and corresponding vcf file.
So I wonder if I can somehow use 1. the reference sequence (B73), 2. gff ot gtf file for it. 3. vcf with data for "my" line. to get cDNA sequences for "my" maize line?

I know, I can apply SNPs to genome of "my" line as follows bcftools consensus -i -s 140903_SND104_A_L007_HDS-1 -H 1 -f ../../agpv3/genome.fa -o s68_ref.fa
cat ../../agpv3/genome.fa | vcf-consensus > s68_ref.fa





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