# Outputs

## seqcluster

- `counts.tsv`: count matrix that can be input of downstream analyses. nloci will be 0 always that the meta-cluster has been resolved successfully. For instance, it can happen that you got sequences you have a bunch of sequences mapping to hundreds of different places on the genome, then seqcluster doesn’t resolve that, and put everything under the larger region covered by those sequences. So, mainly, 0 all are good rows. The ann column is just where the meta-clusters overlap with. It can happen that one name appears many times if different locations of the meta-cluster map to different copies of that feature. OR if the annotation file used had multiple lines for that.

- `read_stats.tsv`: number of reads for each sample after each step in the analysis. Meant to give a hint if we lose a lot of information or not.

- `size_counts.tsv`: size distribution of the small RNA by annotation group. (position, reads, cluster)

- `seqcluster.json`: json file containing all information. This file is used as the input of the report suit.

- `log/run.log`: all messages at debug level

- `log/trace.log`: to keep trace of algorithm decisions

## Report

Beside the static HTML report that you can get using `report` subcommand, you can download this HTML. (watch the repository to get notifications of new releases.)

- Go inside `seqclusterViz` folder

- Open `reader.html`

- Upload the `seqcluster.db` file generated by `report` subcommand.

- Start browsing your data!

Meaning of different sections:

- Top-left table shows list of meta-clusters, user can filter by number ID or keywords.

- Top-right table shows positions where this meta-cluster has been detected.

- Expression profile along precursor: Lines are number of reads in that position of the precursor. It is sum of the log2 RPM of the expression for each sample.

- Table: raw counts for each sample and sequence. Only top 100 are shown.

- secondary structure: The region with more sequences inside meta-cluster is used to plot the secondary structure. Colors refers to abundance in each position. Darker means more abundance.

An example of the HTML code: