Please excuse me for long series of questions, but this is a challenging problem which I have not faced before and trying to troubleshoot. Gene Codes developed the Assemble to Reference Sequence strategy that is widely used to speed up assembly and assign base-numbering systems and features to new data. You should now have two contigs, one that has all the reverse sequences. contig assembly, and custom reporting that is superior in nature to those. the sequence of a gene in both directions using forward and reverse primers. Gene Codes has long been an innovator, investing in the R&D to develop powerful features for your DNA sequence analysis. Highlight all the forward sequences and press the box Assemble Automatically. Accuracy is greater than 99 using Phred 20 bi-directional sequence traces. So does that mean that the assembler did not generate a complete assembly? If that is the case which assembler can I use? will generating assembly from merged reads work? Also, is it possible that the reason this region is not assembled is because it contains repeats? How can I check for repeats (Which tool or strategy to use to check repeats for this region?).Īdditionally, you mentioned annotate the plasmid, how can I do that? Use the instructions below to familiarize yourself with Sequencher software. I also checked the depth at these positions and the average per base coverage is 8212X which I guess is high. I performed a resequencing analysis, in which I mapped the reads to the reference using BWA and performed variant calling apart from 1 insertion of CG at position 6354 and 2 insertions at positions 10384 of 22 bp long and 10349 of 4 bp long, there are no more variants in the consensus sequence.
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