10000 My results looks wrong · Issue #11 · pachterlab/kite · GitHub
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My results looks wrong #11

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saramoein372 opened this issue Dec 28, 2021 · 0 comments
Open

My results looks wrong #11

saramoein372 opened this issue Dec 28, 2021 · 0 comments

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@saramoein372
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Hello Pacher lab,

Thank you so much for sharing your code and helping us to analyze our data; I am analyzing my asap-seq data.
For that purpose, first I used asap-to-kite to preprocess my fastq files; then I am using kallisto|bus for downstream analysis.

This is my feature barcode file:

CCTATTCCGATTCCG CD38_TotSeqA
GCATTGTACGATTCA CD90_TotSeqA
TCAATCCTTCCGCTT CD45RA_TotSeqA
TTCCGAGGATGATCT CD49f_TotSeqA
TGATGGCCTATTGGG HTO2_TotSeqA
AGTAAGTTCAGCGTA HTO4_TotSeqA
TCAGGTCCTTTCAAC CD184_TotSeqA

The problem is after generating my adata file, it only has few rows; which means something is not correct in the way I am running kallisto.

My adata file looks:

adata.obs.head()
Empty DataFrame
Columns: []
Index: [AACAACCCACGATTAC, AACACACCAAACAGGC, AACCAACCAAAGGCCA, AACCAACCAACCCTCT, AACCAACCACGATTAC]

But I am not sure what is wrong. Do you have any suggestions for me? What are the requirements of my inoput data when I am running kalliso|bus tool?

I appreciate your support!

Thank you so much.

Best,
Sara
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