Database used here

[jfouret]

Hi, It is unclear here and in your paper what database you are using at the time you are aligning reads against the reference with bowtie2.

Is the following what you have done ?

1. Reads were aligned against the (i) C.elegans assembled fragment (WS230) + (ii) ERCC spike.
2. Then annotation of the gtf were trimmed (somehow?) to keep only the 3' part

Thanks,

(and sorry by advance if I miss something)

[Puriney]

@jfouret I suggest you email Dr. Yanai for details because I don't know which paper is discussed here, and probably it used the previous generation pipeline (https://github.com/yanailab/CEL-Seq-pipeline) for CEL-Seq/CEL-Seq2.