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salzman-lab / SpliZ

Nextflow implementation of SpliZ
MIT License
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Issue aboout calculating SpliZ #14

Closed tjhwangxiong closed 2 years ago

tjhwangxiong commented 2 years ago

I have four celltype, including CD4T, CD8T, B, NK cells, and three groups, including control, early, late. If I just want to compare differential splicing between control and early within CD4T and CD8T cells. Should I include all groups and celltyes in meta.tsv?

If only barcodes of CD4T and CD8T cells in control and early groups were included in meta.tsv, the SpliZ value will be affected?

cell_id grouping_level_2 grouping_level_1 Control_AAACATTGAGCTAC Control CD8 T Control_AGTACTCTCAACCA Control CD8 T Control_ATGTTCACCGTAGT Control CD4 T Control_CGCTACTGAACAGA Control CD4 T Early_TAGTTAGATGAACC Early CD8 T Early_ACCTATTGTGCCCT Early CD8 T Early_TAGAATTGTATCGG Early CD4 T Early_ATAGATACCATGGT Early CD4 T

or like this

cell_id grouping_level_2 grouping_level_1 Control_AAACATTGAGCTAC Control CD8 T Control_AGTACTCTCAACCA Control CD8 T Control_ATGTTCACCGTAGT Control CD4 T Control_CGCTACTGAACAGA Control CD4 T Early_TAGTTAGATGAACC Early CD8 T Early_ACCTATTGTGCCCT Early CD8 T Early_TAGAATTGTATCGG Early CD4 T Early_ATAGATACCATGGT Early CD4 T Late_TAGTTAGATGAACC Late CD8 T Late_ACCTATTGTGCCCT Late CD8 T Late_TAGAATTGTATCGG Late CD4 T Late_ATAGATACCATGGT Late CD4 T Control_AAACATTGAGCTAC Control NK Control_AGTACTCTCAACCA Control NK Control_ATGTTCACCGTAGT Control NK Control_CGCTACTGAACAGA Control NK Early_TAGTTAGATGAACC Early NK Early_ACCTATTGTGCCCT Early NK Early_TAGAATTGTATCGG Early NK Early_ATAGATACCATGGT Early NK Late_TAGTTAGATGAACC Late NK Late_ACCTATTGTGCCCT Late NK Late_TAGAATTGTATCGG Late NK Late_ATAGATACCATGGT Late NK

Thanks.

wlei-amu commented 2 years ago

I have four celltype, including CD4T, CD8T, B, NK cells, and three groups, including control, early, late. If I just want to compare differential splicing between control and early within CD4T and CD8T cells. Should I include all groups and celltyes in meta.tsv?

If only barcodes of CD4T and CD8T cells in control and early groups were included in meta.tsv, the SpliZ value will be affected?

cell_id grouping_level_2 grouping_level_1 Control_AAACATTGAGCTAC Control CD8 T Control_AGTACTCTCAACCA Control CD8 T Control_ATGTTCACCGTAGT Control CD4 T Control_CGCTACTGAACAGA Control CD4 T Early_TAGTTAGATGAACC Early CD8 T Early_ACCTATTGTGCCCT Early CD8 T Early_TAGAATTGTATCGG Early CD4 T Early_ATAGATACCATGGT Early CD4 T

or like this

cell_id grouping_level_2 grouping_level_1 Control_AAACATTGAGCTAC Control CD8 T Control_AGTACTCTCAACCA Control CD8 T Control_ATGTTCACCGTAGT Control CD4 T Control_CGCTACTGAACAGA Control CD4 T Early_TAGTTAGATGAACC Early CD8 T Early_ACCTATTGTGCCCT Early CD8 T Early_TAGAATTGTATCGG Early CD4 T Early_ATAGATACCATGGT Early CD4 T Late_TAGTTAGATGAACC Late CD8 T Late_ACCTATTGTGCCCT Late CD8 T Late_TAGAATTGTATCGG Late CD4 T Late_ATAGATACCATGGT Late CD4 T Control_AAACATTGAGCTAC Control NK Control_AGTACTCTCAACCA Control NK Control_ATGTTCACCGTAGT Control NK Control_CGCTACTGAACAGA Control NK Early_TAGTTAGATGAACC Early NK Early_ACCTATTGTGCCCT Early NK Early_TAGAATTGTATCGG Early NK Early_ATAGATACCATGGT Early NK Late_TAGTTAGATGAACC Late NK Late_ACCTATTGTGCCCT Late NK Late_TAGAATTGTATCGG Late NK Late_ATAGATACCATGGT Late NK

Thanks.

Hello.Can you run Sicilian tool successfully? If possible, I would like to know whether you use NFcore/Sicilian or install it locally? Whether python=3.6.3 and R=3.6.1 need to be strictly restricted?Thank you very much!

juliaolivieri commented 2 years ago

@tjhwangxiong No need to subset your meta.tsv file. I would maintain it like it is in your second example

tjhwangxiong commented 2 years ago

I have four celltype, including CD4T, CD8T, B, NK cells, and three groups, including control, early, late. If I just want to compare differential splicing between control and early within CD4T and CD8T cells. Should I include all groups and celltyes in meta.tsv? If only barcodes of CD4T and CD8T cells in control and early groups were included in meta.tsv, the SpliZ value will be affected? cell_id grouping_level_2 grouping_level_1 Control_AAACATTGAGCTAC Control CD8 T Control_AGTACTCTCAACCA Control CD8 T Control_ATGTTCACCGTAGT Control CD4 T Control_CGCTACTGAACAGA Control CD4 T Early_TAGTTAGATGAACC Early CD8 T Early_ACCTATTGTGCCCT Early CD8 T Early_TAGAATTGTATCGG Early CD4 T Early_ATAGATACCATGGT Early CD4 T or like this cell_id grouping_level_2 grouping_level_1 Control_AAACATTGAGCTAC Control CD8 T Control_AGTACTCTCAACCA Control CD8 T Control_ATGTTCACCGTAGT Control CD4 T Control_CGCTACTGAACAGA Control CD4 T Early_TAGTTAGATGAACC Early CD8 T Early_ACCTATTGTGCCCT Early CD8 T Early_TAGAATTGTATCGG Early CD4 T Early_ATAGATACCATGGT Early CD4 T Late_TAGTTAGATGAACC Late CD8 T Late_ACCTATTGTGCCCT Late CD8 T Late_TAGAATTGTATCGG Late CD4 T Late_ATAGATACCATGGT Late CD4 T Control_AAACATTGAGCTAC Control NK Control_AGTACTCTCAACCA Control NK Control_ATGTTCACCGTAGT Control NK Control_CGCTACTGAACAGA Control NK Early_TAGTTAGATGAACC Early NK Early_ACCTATTGTGCCCT Early NK Early_TAGAATTGTATCGG Early NK Early_ATAGATACCATGGT Early NK Late_TAGTTAGATGAACC Late NK Late_ACCTATTGTGCCCT Late NK Late_TAGAATTGTATCGG Late NK Late_ATAGATACCATGGT Late NK Thanks.

Hello.Can you run Sicilian tool successfully? If possible, I would like to know whether you use NFcore/Sicilian or install it locally? Whether python=3.6.3 and R=3.6.1 need to be strictly restricted?Thank you very much!

I used bam file as input in Non-sicililan model.

tjhwangxiong commented 2 years ago

@tjhwangxiong No need to subset your meta.tsv file. I would maintain it like it is in your second example

Thanks a lot. I hope your great lab develop some visualization and ploting tools for the summary results. It will greatly help us interpret the results. Thanks

wlei-amu commented 2 years ago

I have four celltype, including CD4T, CD8T, B, NK cells, and three groups, including control, early, late. If I just want to compare differential splicing between control and early within CD4T and CD8T cells. Should I include all groups and celltyes in meta.tsv? If only barcodes of CD4T and CD8T cells in control and early groups were included in meta.tsv, the SpliZ value will be affected? cell_id grouping_level_2 grouping_level_1 Control_AAACATTGAGCTAC Control CD8 T Control_AGTACTCTCAACCA Control CD8 T Control_ATGTTCACCGTAGT Control CD4 T Control_CGCTACTGAACAGA Control CD4 T Early_TAGTTAGATGAACC Early CD8 T Early_ACCTATTGTGCCCT Early CD8 T Early_TAGAATTGTATCGG Early CD4 T Early_ATAGATACCATGGT Early CD4 T or like this cell_id grouping_level_2 grouping_level_1 Control_AAACATTGAGCTAC Control CD8 T Control_AGTACTCTCAACCA Control CD8 T Control_ATGTTCACCGTAGT Control CD4 T Control_CGCTACTGAACAGA Control CD4 T Early_TAGTTAGATGAACC Early CD8 T Early_ACCTATTGTGCCCT Early CD8 T Early_TAGAATTGTATCGG Early CD4 T Early_ATAGATACCATGGT Early CD4 T Late_TAGTTAGATGAACC Late CD8 T Late_ACCTATTGTGCCCT Late CD8 T Late_TAGAATTGTATCGG Late CD4 T Late_ATAGATACCATGGT Late CD4 T Control_AAACATTGAGCTAC Control NK Control_AGTACTCTCAACCA Control NK Control_ATGTTCACCGTAGT Control NK Control_CGCTACTGAACAGA Control NK Early_TAGTTAGATGAACC Early NK Early_ACCTATTGTGCCCT Early NK Early_TAGAATTGTATCGG Early NK Early_ATAGATACCATGGT Early NK Late_TAGTTAGATGAACC Late NK Late_ACCTATTGTGCCCT Late NK Late_TAGAATTGTATCGG Late NK Late_ATAGATACCATGGT Late NK Thanks.

Hello.Can you run Sicilian tool successfully? If possible, I would like to know whether you use NFcore/Sicilian or install it locally? Whether python=3.6.3 and R=3.6.1 need to be strictly restricted?Thank you very much!

I used bam file as input in Non-sicililan model.

Thank you very much！