Artificial intelligence. Has someone used AI scripts running with MPI library for crunching info from large databases? Trying to use MPI with AI.

Hi,

I´m think about pooling strategy for large-scale RNA-seq: what is the best way to allocate many different libraries on multiple flow cells.

For example, there are 40 libraries in total that should be run on 2 flow cells to get necessary coverage. There could be 2 possible strategies:

to make 2 pool A and B with 20 unique libraries in each and run each pool on one flow cell;

to make one pool with 40 libraries and run it on two flow cell.

At the end, when reads are merged, both strategies will lead to the same number of reads per library. Both strategies have technical pros and contras but may be there are some important details that can influence down-stream analysis and have to be considered?

Any thoughts would be greatly appreciated.

I want to sequence the amplicons with two different library prep kits.

1. Nextera DNA Flex Library Prep. kit

2. QIAseq Ultralow Input Library Kit

Can I use the libraries from both preparation kits in a single cartridge simultaneously? If not, what is the possible reason?

Furthermore, is it possible to use the Adapters of one library prep. kit for another?

I’m writing to request your advice about the ATACseq in primary human cells. I am Si Young Lee who is currently working for VRC/NIH. We recently made a pooled library by pooling each 21 library from 7 different samples. I clearly saw the periodicity of the fragment lengths in each library but 3 libraries have different pattern like high peak in high size, #13-15; they are from same sample. Eventually we wan to run a Hiseq but we may run a Miseq first to check a balance of pooled library. I searched several references and all references are really helpful. However, I am not sure if I can use this pooled library to run Miseq because of the different pattern of library in sample #13-15. Do you think this pooled library is good enough to run a Miseq?

Any comments and suggestion will be appreciated.

Thanks

SY

We use the NEBNext Library Quant Kit for Illumina to determine our Illumina library concentrations. Before taking the library to qPCR, we usually run the library on Bioanalyzer to get an idea of the concentration. Based on Bioanalyzer, we will dilute the library down to 5,000pM for qPCR. Most of the time, qPCR results will show libraries around 5,000pM (maybe 4,000-6000pM). In some cases, the qPCR concentration can be double or even triple the Bioanalyzer concentration. When this happens we QC the library by Qubit. In most cases, the Qubit concentration will be similar to the Bioanalzyer concentration.

This makes it challenging for us to determine which concentration to use for loading the sequencer. If we use the qPCR concentration, the runs will be under-clustered. We are trying to understand why we would get higher concentrations from qPCR. It makes more sense if the qPCR concentrations were lower than Qubit/BA suggesting that the adapter ligation was not very successful.

Why do you think we would get such high qPCR concentrations? One thought is that there may be single stranded DNA in the library which is not detected by Qubit or BA, but qPCR is able to amplify. Curious to know your thoughts.

Thank you,

Karrie

What might be the relevance of ICT in design and planning of libraries especially to developing countries

Specifically, how to get good overlap PCR reactions? What steps are critical in good amplification and overlap to build a high titre PD library? Thanks Carlos Prudencio

Does it even make sense to incorporate social media in the provision of library services?  Should libraries just steer clear of this phenomenon or are there ways that this can be used to enhance the current services provided?