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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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Biological replicate #213

Closed AndreaYCT closed 3 months ago

AndreaYCT commented 3 months ago

Hi,

xpore diffmod can calculate " Pairwise comparison without replicates with default parameter setting."

I'd like to maker sure that I can only have two input files. Is it possible to run with biological replicates (two samples for KO and two samples for WT)?

Thanks!

Andrea

yuukiiwa commented 3 months ago

Hi Andrea (tagging you here @AndreaYCT ),

You can add a second replicate like the following:

notes: Pairwise comparison without replicates with default parameter setting.

data:
    KO:
        rep1: ./data/HEK293T-METTL3-KO-rep1/dataprep
        rep2: ./data/HEK293T-METTL3-KO-rep2/dataprep
    WT:
        rep1: ./data/HEK293T-WT-rep1/dataprep
        rep2: ./data/HEK293T-WT-rep2/dataprep

out: ./out

Thanks!

Best wishes, Yuk Kei

AndreaYCT commented 3 months ago

Hi Andrea (tagging you here @AndreaYCT ),

You can add a second replicate like the following:

notes: Pairwise comparison without replicates with default parameter setting.

data:
    KO:
        rep1: ./data/HEK293T-METTL3-KO-rep1/dataprep
        rep2: ./data/HEK293T-METTL3-KO-rep2/dataprep
    WT:
        rep1: ./data/HEK293T-WT-rep1/dataprep
        rep2: ./data/HEK293T-WT-rep2/dataprep

out: ./out

Thanks!

Best wishes, Yuk Kei

Hi, @yuukiiwa,

In this case, I can have as many replicates as I wish, and I only can compare two exp groups, right?

Andrea

yuukiiwa commented 3 months ago

Hi Andrea (tagging you here @AndreaYCT),

You can have as many groups and replicates as you want as follows. Just that the more groups you include, the longer xpore diffmod will run due to the increasing number of pairwise comparisons.

data:
    groupA:
        rep1: ./data/A1/dataprep
        rep2: ./data/A2/dataprep
    groupB:
        rep1: ./data/B1/dataprep
        rep2: ./data/B2/dataprep
    groupC:
        rep1: ./data/C1/dataprep
        rep2: ./data/C2/dataprep
    groupD:
        rep1: ./data/D1/dataprep
        rep2: ./data/D2/dataprep

out: ./out

Thanks!

Best wishes, Yuk Kei

AndreaYCT commented 3 months ago

Hi Andrea (tagging you here @AndreaYCT),

You can have as many groups and replicates as you want as follows. Just that the more groups you include, the longer xpore diffmod will run due to the increasing number of pairwise comparisons.

data:
    groupA:
        rep1: ./data/A1/dataprep
        rep2: ./data/A2/dataprep
    groupB:
        rep1: ./data/B1/dataprep
        rep2: ./data/B2/dataprep
    groupC:
        rep1: ./data/C1/dataprep
        rep2: ./data/C2/dataprep
    groupD:
        rep1: ./data/D1/dataprep
        rep2: ./data/D2/dataprep

out: ./out

Thanks!

Best wishes, Yuk Kei

That's so cool!! Thanks for developing such a good tool!

Andrea