Question: What are the differences between RNA-Seq and Single Cell RNA Seq with respect to Sequence Analysis
1
gravatar for ayyappakumar.s
4.6 years ago by
ayyappakumar.s20 wrote:

What are the differences between RNA-Seq and Single Cell RNA Seq with respect to Sequence Analysis

a) As it is generating fasq files of huge size

  For Ex: I have downloaded the fastq files (paired end data) for C.elegans from SRA it turned out to be 52.3 GB

b) The composition of bases are of T bases, Why ? (Preliminarily)

 

rna-seq • 2.3k views
ADD COMMENTlink modified 4.6 years ago by Michele Busby2.0k • written 4.6 years ago by ayyappakumar.s20
2
gravatar for Michele Busby
4.6 years ago by
Michele Busby2.0k
United States
Michele Busby2.0k wrote:

For a start:

The main difference is that you usually have to divide your reads by some sort of barcode to get which reads belong to which cell.  

The barcode will need to be trimmed off before aligning, but from there the basic alignment and quantification steps are the similar with each cell treated like its own sample.

Also, each cell is usually sequenced more shallowly than a library because there are fewer molecules in the input, so you start getting duplicate reads earlier earlier.  You may want to remove duplicates, like with Picard.

There might be a lot of runs of Ts if they were sequencing into the poly a tail a lot.  It would depend on the protocol.  I do not think it is a problem inherent to the fact that it is single cell.  That happens sometimes with regular libraries.

The downstream analyses are different.  I would look up Rahul Satija's papers.  He has got some analyses he has done and he has a package for single cell stuff.  I do not know how available it is yet.

ADD COMMENTlink written 4.6 years ago by Michele Busby2.0k
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