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Issues with hashsolo #79

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st4302 opened this issue Apr 25, 2023 · 0 comments
Closed

Issues with hashsolo #79

st4302 opened this issue Apr 25, 2023 · 0 comments

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@st4302
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st4302 commented Apr 25, 2023

I tried to run hashsolo after cellranger count with feature barcode data but I am having some issues. Below is how I tried to use it.

Sample1= sc.read_10x_h5('filtered_feature_bc_matrix.h5', gex_only=False)
Sample1.var_names_make_unique()
Sample1.layers["counts"] = Sample1.X.copy()
sc.pp.filter_genes(Sample1, min_counts=1)
hashtags_Sample1=Sample1[:,Sample1.var_names.str.startswith('TotalSeq')].copy()

hashtags_Sample1
AnnData object with n_obs × n_vars = 8714 × 5
    var: 'gene_ids', 'feature_types', 'genome', 'n_counts'
    layers: 'counts'
hashtags_Sample1.var
	gene_ids	feature_types	genome	n_counts
TotalSeq-B0301_anti-mouse_Hashtag_1_Antibody	B0301	Antibody Capture		469979.0
TotalSeq-B0302_anti-mouse_Hashtag_2_Antibody	B0302	Antibody Capture		1215844.0
TotalSeq-B0303_anti-mouse_Hashtag_3_Antibody	B0303	Antibody Capture		2017272.0
TotalSeq-B0304_anti-mouse_Hashtag_4_Antibody	B0304	Antibody Capture		628403.0
TotalSeq-B0305_anti-mouse_Hashtag_5_Antibody	B0305	Antibody Capture		126639.0

hashsolo.hashsolo(hashtags_Sample1)
Sample1.obs['most_likely_hypothesis'] = hashtags_Sample1.obs['most_likely_hypothesis']
Sample1.obs['Classification'] = hashtags_Sample1.obs['Classification']

sc.pl.highest_expr_genes(Sample1, n_top=20, )

However, once I do to the sc.pl.highest_expr_genes step I get the hashtags in the plot. Have I done something wrong? I did notice that when I uploaded the h5 file my hashtags are actually in the .var column.

Thank you

@st4302 st4302 closed this as completed Apr 26, 2023
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