Hi everyone,
I'm assemblying a genome from contigs and pacbio data. The contigs were assembled from Illumina paired-end reads. And the pacbio data were in fasta file and were corrected by Illumina reads with LoRDEC v0.6. Therefore, the basepair in fasta were a mixture of upper nucleotide (ATCG) and lower nucleotide (atcg). The upper nucleotide were corrected sequences and lower nucleotide were not corrected by Illumina reads. The example is as following:
Now I want to prepare quality file for this corrected fasta file, but I found fakeQuals.py can only give the same quality for all nucleotide in one fasta file. I'm wondering whether there is a software that can give different qualtiy for upper nucleotide and lower nucleotide in one fasta file? Thanks
Beide
Last edit: Beide 2016-03-29
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I've wrote a shell script to do the job above. But which value should I give for the uncorrected nucleotide (atcg) and the corrected nucleotide (ATCG)?
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi everyone,
I'm assemblying a genome from contigs and pacbio data. The contigs were assembled from Illumina paired-end reads. And the pacbio data were in fasta file and were corrected by Illumina reads with LoRDEC v0.6. Therefore, the basepair in fasta were a mixture of upper nucleotide (ATCG) and lower nucleotide (atcg). The upper nucleotide were corrected sequences and lower nucleotide were not corrected by Illumina reads. The example is as following:
Now I want to prepare quality file for this corrected fasta file, but I found fakeQuals.py can only give the same quality for all nucleotide in one fasta file. I'm wondering whether there is a software that can give different qualtiy for upper nucleotide and lower nucleotide in one fasta file? Thanks
Beide
Last edit: Beide 2016-03-29
I've wrote a shell script to do the job above. But which value should I give for the uncorrected nucleotide (atcg) and the corrected nucleotide (ATCG)?
PBJelly doesn't rely on fastq base qualities, so whatever values you fake for your sequences will be fine.