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tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://nanocompore.rna.rocks
GNU General Public License v3.0
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Analyze the nanocompore result #151

Closed aman21392 closed 3 years ago

aman21392 commented 3 years ago

Hi, I just posted the final results of my nanocompore analysis. But i didn't understand on which basis i consider it m6A modified and unmodified. So please can you help me to sort out this issue. Thanks in advance. pos chr genomicPos ref_id strand ref_kmer GMM_logit_pvalue KS_dwell_pvalue KS_intensity_pvalue GMM_cov_type GMM_n_clust cluster_counts Logit_LOR 13 NA NA ENST00000651669.1 NA GACGA 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:13/1Condition2_1:5/0 0.15415067982725816 14 NA NA ENST00000651669.1 NA ACGAC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 15 NA NA ENST00000651669.1 NA CGACC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 16 NA NA ENST00000651669.1 NA GACCT nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 17 NA NA ENST00000651669.1 NA ACCTA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 18 NA NA ENST00000651669.1 NA CCTAC 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:27/3Condition2_1:4/2 1.4350845252893225 19 NA NA ENST00000651669.1 NA CTACG nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 20 NA NA ENST00000651669.1 NA TACGC 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:7/23Condition2_1:4/2 -1.6094379124341005 21 NA NA ENST00000651669.1 NA ACGCA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 22 NA NA ENST00000651669.1 NA CGCAC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 23 NA NA ENST00000651669.1 NA GCACA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 24 NA NA ENST00000651669.1 NA CACAC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 25 NA NA ENST00000651669.1 NA ACACG nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 26 NA NA ENST00000651669.1 NA CACGA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 27 NA NA ENST00000651669.1 NA ACGAG 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:6/24Condition2_1:1/5 -0.1743533871447777 28 NA NA ENST00000651669.1 NA CGAGA 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:23/6Condition2_1:6/0 -0.7137664677626812 29 NA NA ENST00000651669.1 NA GAGAA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 30 NA NA ENST00000651669.1 NA AGAAC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 31 NA NA ENST00000651669.1 NA GAACA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 32 NA NA ENST00000651669.1 NA AACAT nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 33 NA NA ENST00000651669.1 NA ACATG 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:23/6Condition2_1:3/3 1.2321436812926319 34 NA NA ENST00000651669.1 NA CATGC 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:8/21Condition2_1:1/5 0.20479441264601259 35 NA NA ENST00000651669.1 NA ATGCC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 36 NA NA ENST00000651669.1 NA TGCCT 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:21/9Condition2_1:2/4 1.299282984130261 37 NA NA ENST00000651669.1 NA GCCTC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 38 NA NA ENST00000651669.1 NA CCTCT nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 39 NA NA ENST00000651669.1 NA CTCTC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 40 NA NA ENST00000651669.1 NA TCTCG nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 41 NA NA ENST00000651669.1 NA CTCGC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 42 NA NA ENST00000651669.1 NA TCGCA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 43 NA NA ENST00000651669.1 NA CGCAA 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:15/14Condition2_1:4/2 -0.4462871026284194 44 NA NA ENST00000651669.1 NA GCAAA 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:28/1Condition2_1:6/0 0.7282385003712155 45 NA NA ENST00000651669.1 NA CAAAG nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 46 NA NA ENST00000651669.1 NA AAAGG nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 47 NA NA ENST00000651669.1 NA AAGGA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 48 NA NA ENST00000651669.1 NA AGGAT nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 49 NA NA ENST00000651669.1 NA GGATC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 50 NA NA ENST00000651669.1 NA GATCT nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 51 NA NA ENST00000651669.1 NA ATCTC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 52 NA NA ENST00000651669.1 NA TCTCC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 53 NA NA ENST00000651669.1 NA CTCCT nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 54 NA NA ENST00000651669.1 NA TCCTT nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 55 NA NA ENST00000651669.1 NA CCTTC 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:9/20Condition2_1:3/3 -0.7419373447293769 56 NA NA ENST00000651669.1 NA CTTCA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 57 NA NA ENST00000651669.1 NA TTCAT nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 58 NA NA ENST00000651669.1 NA TCATC 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:21/9Condition2_1:6/0 -1.1574527886910433 59 NA NA ENST00000651669.1 NA CATCC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 60 NA NA ENST00000651669.1 NA ATCCC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 61 NA NA ENST00000651669.1 NA TCCCT nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 62 NA NA ENST00000651669.1 NA CCCTC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 63 NA NA ENST00000651669.1 NA CCTCT 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:5/25Condition2_1:1/5 -0.36772478012531673 64 NA NA ENST00000651669.1 NA CTCTC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 65 NA NA ENST00000651669.1 NA TCTCC nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 66 NA NA ENST00000651669.1 NA CTCCA nan 0.9999999997843159 0.9999995600113659 full 1 NC NC 67 NA NA ENST00000651669.1 NA TCCAG 0.9997766988324855 0.9999999997843159 0.9999995600113659 full 2 Condition1_1:24/4Condition2_1:5/0 -0.18232155679395445

tleonardi commented 3 years ago

Hi @aman21392, you should look at the pvalue columns (in particular GMM_logit_pvalue). When these p-values are below a significance threshold (e.g. 0.01) you can consider that position to be modified. Please look at our paper on bioRxiv for info on how these tests are run.