trimming 75bp long reads for denovo assembly

Question

[mike]

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

[GenoMax]

First 11 bp may be due to a bias caused library prep.

Answer 1

[Brice Sarver]

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.