Hi All, I just submitted a manuscript for metatranscripomic analysis results based on one of the SRA study. I was reporting some of the sequences from Trinity assembly for this study. I just got some comments from the reviewers saying that I missed to report some additional contigs. One of the reviewers was able to find additional contigs that I was not able to find in Trinity assembled database. I then alligned the fastq files (paired end) to the contigs reviewers found. I found that it has less than three hundred reads aligned. I could not find those contigs in my Trinity assembled database, but I was still able to align fastq reads (albeit less than 300 reads) to those contigs. Therefore, I was wondering if Trinity has failed to report those contigs with low coverage. Does Trinity drop the contigs with low coverge during de-novo assembly? Would anyone please help me understand why it was not reported by Trinity so I could write my rebuttal to them?
Question: What is the fate of low coverage region during Trinity assembly of transcriptome data?
6 months ago by
MAPK • 1.4k
MAPK • 1.4k wrote:
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