trimming 75bp long reads for denovo assembly
Hi,
I have Mice samples with 75 bp paired reads and I am interested in doing de novo assembly for detecting novel long non-coding RNAs. In the Quality control plots, I can see that the first 11 reads are needed to be trimmed. I was wondering if it is a good idea to trim initial reads and proceed with 64 bp (75bp - 11bp) reads.
Please advise me on this.
Thanks
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Brice Sarver
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mike
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mike
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If the bases are low quality or contain residual adapters, the answer is almost always yes. For assembly, such bases will just confound the k-mer graph or prevent reads from overlapping that should. If they're resulting from a bias in the library preparation (and these are, therefore, good bases), you should include them.
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First 11 bp may be due to a bias caused library prep.