50 bp Single end Vs 100 bp Single end Vs 50 bp Paired end

[dhanapala]

Hi

I have planned to do RNAseq in Soybean with 3 biological replicates

May i know which type of sequencing would be the right one (Hi seq), if i would like to see the

SNP difference
Gene expression
Differential expression and
Splice junctions

[dpryan]

For SNP calling you need to mark PCR duplicates. That works better with paired-end reads, so of the options I'd do 50bp paired-end. Paired-end reads will also be beneficial for mapping in general. You'll also be better able to differentiate isoforms with paired-end reads, if that's important to you.

[dhanapala]

Thanks dpryan

Since we have reference genome for Soybean

So do you mean the 50bp PE is good option and still all above four analysis can be done ?

How about the exon expression ? Is it possible too ?

[alexdobin]

I would recommend doing 2x100bp

Paired-end reads are preferred for de-convolution of isoform expression such as done by Cufflinks.
On the other hand, longer reads allow for much more accurate detection of the splice junctions.

[adaptivegenome]

PE first priority, longer reads second. Any reason you can't do 100?