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Hi
I am preparing Illumina libraries using two separate protocols from NEB - one does a size selection step and one just cleans up after adapter ligation.
Bottom line of this is that instead of getting a library from 200-400bp with a beak at ~240bp after the final PCR, I get a smear with roughly the same peak but the width is 200-700bp (see attached figure).
Before I decide if I can go with their alternative protocol I am trying to understand how the wide peak may affect my downstream bioinformatics? I need to do two things with the libraries - one is a differential expression analysis between samples; the other is transcriptome assembly and then DE (two completely different experiments).
thanks!
I am preparing Illumina libraries using two separate protocols from NEB - one does a size selection step and one just cleans up after adapter ligation.
Bottom line of this is that instead of getting a library from 200-400bp with a beak at ~240bp after the final PCR, I get a smear with roughly the same peak but the width is 200-700bp (see attached figure).
Before I decide if I can go with their alternative protocol I am trying to understand how the wide peak may affect my downstream bioinformatics? I need to do two things with the libraries - one is a differential expression analysis between samples; the other is transcriptome assembly and then DE (two completely different experiments).
thanks!