Hello, I was wondering with IDBA-Tran they want you to have a .fasta file as input. I converted my file from .fastq to .fasta but I noticed in their example conversion they also filter out reads with NNNs in them. How important is this for proper assembly of the transcriptome? Thanks.
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It is always an option to clean your reads of NNN and other low quality reads, but you don't need to, for this and other assemblers. De-novo assemblers do internally use higher quality reads instead of poor ones where available. I do both ways sometimes, but current Illumina sequencer outputs are generally high quality.
I get good transcript assemblies with idba-trans, with a caveat that I use all the kmer-set "transcripts-kk.fa" outputs, rather than IDBA's final "merged" set, which has poorer gene completeness than the per-kmer sets.
Find here a comparison of 4 gene assemblers, used in EvidentialGene's production of highly accurate gene reconstructions for the malaria mosquito and yellow fever/Zika mosquito:
idba_trans comes in second best, after velvet/oases the reigning champion of gene assembly. idba_trans uses less memory and runs faster than velvet/oases, and the authors' paper helps explain why it and velvet/oases do so well with multi-kmer constructions of the variably expressed genes and their alternate transcripts. Please consider using http://eugenes.org/EvidentialGene/ methods along with several gene assemblers to obtain highly accurate animal and plant gene sets.
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