Differential expression analysis of the Socs3 knockout data

Aim: Investigate the differences in gene expression between wild-type samples and Socs3 knockout samples.

Samples:

We have 6 mice samples, 3 are wild-type and 3 are Socs3 knockout samples. The data is bulk RNA-sequencing from bone.

• WT: Wild-type.
• SOCS3: Socs3 gene knockout.

Each sample was sequenced across 8 lanes.

Batches:

There are 2 batches.

• Batch1: 2 WT samples, 2 SOCS3 samples.
• Batch2: 1 WT sample, 1 SOCS3 sample.

Alignment tools

We tried out a few different pre-processing pipelines for this data. I have split them into broad categories based on the tool used for the alignment step.

• kallisto: Transcript-based method of alignment, more recommended currently.
• Hisat2: Gene-based method, not as commonly used anymore.