I have tested LoRDEC with the ecoli data and get some useful information. However when I tried LoRDEC with elegans data, it does not work out the expected result.The error rate is still at a very high level and is almost the same as the original long reads.
The pacbio data is download from : http://datasets.pacb.com.s3.amazonaws.com/2014/c_elegans/list.html I choose to combine the fastq files in 40X/raw_data/2590970/0001/Analysis_Results/ into one fastq file and use it as long pacbio reads.
The illumina read is donwload using sratoolkit form ncbi with the commend: ./fastq-dump.2.8.2 SRR065390.
The reference sequence is chrom 1 of elegans download form ncbi.
I am wondering if I use the proper data and why after LoRDEC error correction the error rate is still as high as the original reads.(The similar situation happens when I apply it to the Yeast data,but it does work on the ecoli data )
Thanks a lot if you can help me solve the problem.
