2 runs per sample

Question

[santosh.bicnehu]

Dear All,

Kindly help me on how to proceed to assemble RNA seq data with 2 runs per sample. My data comprises of 4 samples with 2 runs for each downloaded from SRA.

Should I merge forward and reverse of first run with the forward and reverse of the second run or assemble them separately and then merge for downstream analysis

[Ram]

Have you tried reading up on any RNAseq analysis workflows online? Please show us that you have invested some effort to solve your problem.

[santosh.bicnehu]

Thanks for your reply. I am new to this and want to learn and explore. your suggestion may help me to understand the area in a broader way

[WouterDeCoster]

Do you mean alignment, or actually doing assembly? Which software are you using?

[santosh.bicnehu]

Thanks for your reply. I want to assemble the reads using trinity

Answer 1

[WouterDeCoster]

For assembly it will be beneficial to have all data available at the same time, so in this case you should merge the reads per direction, which you can do with cat.

[GenoMax]

In addition, use the same order of file names when cating to be safe.