trancriptome analysis using rna-seq data

Question

[murmu.sneha22]

Can anyone please suggest me what software tools should I use for the trancriptome analysis using RNA-seq data obtained from SOLiD? I mean. are the downstream analysis tools sequencing platform-specific? Can I use Tuxedo protocol (Tophat+Cufflink) for the same objective or is it exclusively meant for Illumina?

Answer 1

[Satyajeet Khare]

You can use Tuxedo protocol. Just check if your raw reads are color space or base space. The protocol is slightly different for each. If your reads are base calls, protocol is similar to Illumina. You can convert colorspace to base space, but I think it is not recommended.

Answer 2

[murmu.sneha22]

Thank you for the help. I've colorspace format. So, will it be appropriate to transform it into basespace format and proceed with Tuxedo? And if not, what are the other option I am left with?

[Satyajeet Khare]

No need to convert to basespace. Just remember Bowtie2 is not compatible with colorspace. Use Bowtie version 0.12.7. Use it for genome indexing as well as alignment.

Answer 3

[murmu.sneha22]

@Satya Okay. Thanks a lot.

[WouterDeCoster]

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