Computed sample attributes
==========================

The expression data in this folder were generated with a version of the RGD RNA-seq workflow earlier than 2.1
and are unchanged. Sample sex, library strandedness and library preparation method were determined
afterwards for these data, using the rules of RGD workflow 2.1. Results are in
<GSE>_computed_sample_attributes_GRCr8.txt and in the JBrowse session ("Computed Sex",
"Computed Strandedness" and "Computed Library Capture").

Sex: sex was previously assigned by curators from the X:Y chromosome coverage ratio and by manually reviewing
the expression of sex-specific genes. This has been codified as a rule:
 R = (Xist TPM + 1) / (median TPM of Uty, Ddx3y, Kdm5d and Eif2s3y + 1);
 R >= 10 is called female, R <= 1 male, and other values Undetermined.
Samples where the rule differed from the earlier call were reviewed by a curator.
Sex in this file is based on the TPM values from the original (pre-2.1) processing.

Strandedness and library preparation: a subset of each sample's reads (3 million reads or read pairs)
was aligned to GRCr8 with STAR to count reads on each strand of every gene. Strandedness is inferred
from the proportion of reads on the sense and antisense strands. Library preparation (poly(A)
selection or rRNA depletion) is inferred from the number of reads on small RNA genes lacking stable
poly(A) tails per million gene-assigned reads (<= 350 poly(A) selection, >= 700 rRNA depletion, values
between reported as ambiguous). These counts were used only for these calls; the expression values
were not changed.

Columns: SampleID, InputSex (submitted to GEO), ComputedSex, XYRatio (not recalculated for these
studies: NA), Agreement (ComputedSex vs. InputSex), TPM of Xist, Uty, Sry, Ddx3y, Kdm5d and Eif2s3y,
ComputedStrand, ComputedLibraryPrep, mapping and coverage metrics of the read subset (PctMRNA,
PctIntronic, PctIntergenic, PctRibosomal, UniqPct, MultiPct, TooShortPct), NonPolyA_perM (the value
the library preparation call is based on), LibraryPrepRule, LibraryPrepQC and LibraryPrepReason.