Open jimmyzhen opened 2 years ago
For RNA-seq thefeature_id
was taken as the ENSEMBL Gene ID
The following process was initially taken to map unique feature_id
s to vial labels:
results
directory was taken. Decision was made to use all tables and not just the normalized-log-cpm
table since some feature_id
to vial label mappings were missing from the normalized-log-cpm
table.feature_ids
and viallabels
. feature_ids
corresponds to a list of any ID-like strings that refer to a particular feature. viallabels
corresponds to a list of samples which show a particular feature.The script used to do the above can be found in the infrastructure utilities repo.
@cteng585, thank you for the _feature_id to viallabels lookup/mapping tables for the rna-seq
tissues!
Suggestions to naming convention for the following keys in any subsequent tables you will create for other assays:
viallabels
changed to vial_labels
Furthermore, my understanding is that, at least for rna-seq
, the mapping would be one unique feature_id
associated with a list of vial-labels
. So can you elaborate on your decision of defining the feature_ids
value as a list of any ID-like strings that refer to a particular feature? What is "any ID-like strings" referring to?
Lastly, since you used all tables in this regard, I wanna confirm that you accounted for potential duplicate feature IDs spanning across different tables.
@cteng585 I've taken a look at a selected sample of the revised rna-seq
lookup tables. Great work! Thank you!
Update:
Revised file input to be from the analysis
directory for genomics data. Per the pipelines team, using files from analysis should remove any outlier data points or samples removed for other QC reasons.
Due to Nicole's work on mapping feature IDs the consortium uses to more standardized features, the alternative_ids
key has been removed from the JSON output. JSON output now only has two keys:
feature_id
: a string identifying the specific feature IDvial_labels
: an array containing the vial_labels expressing a specific feature IDfeature_ID
will be the first column of the normalized-log-cpm
table as there is not a well-labeled feature ID column
Code for the mapping table script can be found in the bic-infrastructure-utilities
repo.
To connect the PASS1B-06 DEA results data to the phenotypic data, we need to map each unique
feature_id
(present in the DEA results) to a list of associatedvial_label
(present in the phenotypic data) for each of the tissues in a given assay.The 2 column mapping table potentially consist of just the
feature_id
andvial_labels
fields, while the source file from which the needed data can be extracted forrna-seq
is from the*-rna-seq_normalized-log-cpm.txt
result file produced by pipeline.