SOLID color-space RNAseq alignment

Question

[lkmklsmn]

Hi,

I have worked with RNAseq data before but this is my first time dealing with SOLID data. I have fastq files in color-space and I would like to align them to the human genome. Which program will allows me to deal with color-space data? Do I need a color-space reference genome? Where do I get one from?

Thanks

Answer 1

[predeus]

This is probably a very late reply, but might be useful to others. SOLID is a platform that's not supported since 2013, so there's not much modern development - however, there's certainly lots of legacy data.

To do unspliced alignment to a genome or transcriptome of short colorspace reads, you can use bowtie (not bowtie2, since it does not support the colorspace indexing), or any of the SOLID-specific programs like SHRIMP. However I would not recommend the latter, since they are very poorly supported. Bowtie v1 is probably your best option right now. You'll need a regular genome sequence, but you have to generate a colorspace-specific reference index (using -C option).

To do spliced genomic alignment, your option is tophat or tophat2, but with bowtie v.1 only.