Hello all,
Our lab is about to undertake a large transcriptome sequencing project where we will be doing both de novo assembly of transcriptomes and RNA-seq comparisons across and within species and we are trying to make some decisions on which tech to use. We have direct access to the new SOLID 5500 and are considering using that for our project (as opposed to the Illumina HiSeq which would probably be a little more expensive and have longer turn-around times). If we run on this machine, we have the option of getting back a variety of different types of data: short read color-space, short read in base-space (new feature), and paired-end short read in color-space. From what I understand, I am inclined to favor the last option as it seems paired-end info will help a lot with ambiguities in assembly and mapping to any subsequently identified isoforms; however, I often hear non-specific grumblings and frustrations with color-space data and skepticism about color-space assembly in particular (obviously has advantages with anything involving SNPs) and am concerned that getting data back in color-space may pose problems down the line. Anyone got any advice on this or comment that might be of use?
Thanks in advance.
Our lab is about to undertake a large transcriptome sequencing project where we will be doing both de novo assembly of transcriptomes and RNA-seq comparisons across and within species and we are trying to make some decisions on which tech to use. We have direct access to the new SOLID 5500 and are considering using that for our project (as opposed to the Illumina HiSeq which would probably be a little more expensive and have longer turn-around times). If we run on this machine, we have the option of getting back a variety of different types of data: short read color-space, short read in base-space (new feature), and paired-end short read in color-space. From what I understand, I am inclined to favor the last option as it seems paired-end info will help a lot with ambiguities in assembly and mapping to any subsequently identified isoforms; however, I often hear non-specific grumblings and frustrations with color-space data and skepticism about color-space assembly in particular (obviously has advantages with anything involving SNPs) and am concerned that getting data back in color-space may pose problems down the line. Anyone got any advice on this or comment that might be of use?
Thanks in advance.
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