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
So I wonder if I can somehow use 1. the reference sequence (B73), 2.
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 AGPv3.fasta.mp.bcf.MUT.filt.vcf.gz -o s68_ref.fa
cat ../../agpv3/genome.fa | vcf-consensus AGPv3.fasta.mp.bcf.MUT.filt_S68.vcf.gz > s68_ref.fa
• 263 views