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Old 10-06-2016, 12:25 AM   #2
Persistent LABS
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Location: Pune, India

Join Date: Apr 2016
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Hi SDPA_Pet,
The length cutoff will depend upon how much you gain while aligning the reads to genome [if your experiment is not a denovo assembly]. Smaller read lengths will increase the chance of alignments at multiple loci, which might not help you.
You can refer this publication: An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis [http://journals.plos.org/plosone/art....pone.0085024]. The authors have used 70% of original read length as the length cutoff.
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