Pre-Processing of SICILIAN Output

[apdavid]

Thank you again for all the help so far, @juliaolivieri. I have the SICILIAN output file, in my case: runname_with_postprocessing.txt and I have a few questions about preparing the data for SpliZ

1. I merged the output file with a file the corresponds to the clusternames (in our case '0-14' as free_annotation) cross-referenced by the cell name. Is that correct? Is it okay to pass number labels, or do they have to be strings? Ex instead of '9' something like 'S9'.
2. Do I need to perform any filtering steps with the following fields: postprocess_passed or both_ann or called prior to running through SpliZ?
3. Should I filter the chrR1A to only those who's names start with chr? There are some that are formatted like this: NT_039192.2
4. Are there any other processing steps required?

[juliaolivieri]

Great questions! I think Kaitlin is helping you with 1 on the other github page. For 2, no need to perform any filtering yourself, the SpliZ pipeline will filter on the called column automatically. For 3, no need to filter out "non-standard" chromosomes, they won't affect the results for the "standard" chromosomes. And for 4, there shouldn't be any other processing steps necessary. Let me know if you run into more issues!

[apdavid]

Thank you this is super helpful. Do I need to filter by postprocess_passed since that variable isn't passed to to SpliZ?

[juliaolivieri]

No need to filter, the called column is the only one from SICILIAN that should be used to filter (and that's already incorporated into the pipeline)

[apdavid]

Okay got it thank you!