Open saramoein372 opened 2 years ago
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
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