Workflow: HPC RGD paired-end workflow 2.1.2. Note: ComputedSex is called from sex-gene expression: R = (Xist TPM + 1) / (median TPM of Uty, Ddx3y, Kdm5d and Eif2s3y + 1); R >= 10 is called F, R <= 1 is called M, and other values, or samples where Xist and the Y-gene median are both below 1 TPM, are Undetermined. Females express Xist and males the Y-linked genes. Sry is reported but not used in the calculation. XYRatio (X:Y read coverage) is shown for reference only. Agreement compares ComputedSex with InputSex (submitted to GEO).
SampleID	InputSex	ComputedSex	XYRatio	Agreement	Xist	Uty	Sry	Ddx3y	Kdm5d	Eif2s3y	ComputedStrand	ComputedLibraryPrep	PctMRNA	PctIntronic	PctIntergenic	PctRibosomal	UniqPct	MultiPct	TooShortPct	NonPolyA_perM	LibraryPrepRule	LibraryPrepQC	LibraryPrepReason
GSM8187629	not_specified	M	26.910913	Conflict	2.66	3.38	0.00	26.64	6.21	24.16	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.891695	0.069238	0.031659	0.007408	90.20	3.97	5.33	77	LP2 (2026-09-30)	PASS	NonPolyA_perM 77 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187630	not_specified	M	21.859538	Conflict	8.30	1.78	0.00	15.48	3.73	13.42	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.901518	0.053457	0.039813	0.005213	89.67	3.26	6.46	35	LP2 (2026-09-30)	PASS	NonPolyA_perM 35 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187631	not_specified	Undetermined	22.391785	Conflict	17.47	2.45	0.00	20.38	5.01	22.69	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.884374	0.070239	0.037348	0.008039	88.41	4.02	6.90	58	LP2 (2026-09-30)	PASS	NonPolyA_perM 58 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187632	not_specified	M	24.130890	Conflict	6.95	1.50	0.00	11.73	3.33	12.45	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.896812	0.054344	0.040832	0.008012	90.07	3.48	5.83	40	LP2 (2026-09-30)	PASS	NonPolyA_perM 40 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187633	not_specified	M	27.563342	Conflict	0.36	2.69	0.00	25.23	6.80	21.98	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.885289	0.07194	0.034624	0.008147	89.97	4.00	5.50	71	LP2 (2026-09-30)	PASS	NonPolyA_perM 71 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187634	not_specified	Undetermined	23.469026	Conflict	12.49	1.68	0.00	14.86	3.76	15.63	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.887912	0.066243	0.040397	0.005448	89.99	3.33	6.00	50	LP2 (2026-09-30)	PASS	NonPolyA_perM 50 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187635	not_specified	M	28.621739	Conflict	0.51	3.34	0.00	24.63	6.44	23.06	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.891855	0.067366	0.034638	0.006141	89.77	3.49	6.26	69	LP2 (2026-09-30)	PASS	NonPolyA_perM 69 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187636	not_specified	Undetermined	20.162162	Conflict	15.80	1.53	0.00	16.84	3.39	13.29	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.888551	0.064659	0.040228	0.006562	89.86	3.59	5.81	54	LP2 (2026-09-30)	PASS	NonPolyA_perM 54 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187637	not_specified	M	25.813852	Conflict	2.09	3.03	0.00	26.89	6.56	22.76	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.887886	0.0697	0.036071	0.006342	90.15	3.56	5.70	72	LP2 (2026-09-30)	PASS	NonPolyA_perM 72 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does