apraga/org - Change 7QQOACUMLIEIUWIGG2WPUUBY6FG3XCNK7CYY4GIZCRY7KSSQIVSQC

Bisonex : starting to get some stats

Created by Alexis Praga on February 19, 2023

7QQOACUMLIEIUWIGG2WPUUBY6FG3XCNK7CYY4GIZCRY7KSSQIVSQC

Dependencies

In channels

main

Change contents

Replacement in projects/bisonex.org at line 2889 [5.35]

B:BD[3.834] → [4.4687:4737]

****** TODO Utiliser seulement exons BestRefSeq

[3.834]

[3.883]

****** Erreur dans le paramètre : -f au lieu de -R !!
Il faut supprimer les overlap (et trier avant)
 bedtools sort -i illumina_exons.bed > illumina_exons.bed.sorted
 bedtools merge -i illumina_exons.bed.sorted > HG001_GRCh38_1_22_v4.2.1_benchmark_illumina_exons.be
******* rtg tools
Threshold  True-pos-baseline  True-pos-call  False-pos  False-neg  Precision  Sensitivity  F-measure
----------------------------------------------------------------------------------------------------
    3.000               1015            910        206      32531     0.8154       0.0303     0.0583
     None               1015            910        206      32531     0.8154       0.0303     0.0583
****** TODO Utiliser seulement exons
******* DONE BestRefSeq 
CLOSED: [2023-02-19 Sun 12:05]

Replacement in projects/bisonex.org at line 2916 [5.35]

B:BD[3.1610] → [2.6951:7071]

******* TODO Tests après correction bug dans noms de chromosome : precision ~ ok, recall très mauvais -> trop de FN ?

[3.1610]

[2.7071]

******** DONE Tests après correction bug dans noms de chromosome : precision ~ ok, recall très mauvais -> trop de FN ?
CLOSED: [2023-02-19 Sun 12:05]

Replacement in projects/bisonex.org at line 2929 [5.35]

B:BD[2.8382] → [2.8382:8456]

******* Vérifier exons
On a l'union des exons de tous les transcripts...

[2.8382]

[2.8456]

******** DONE Vérifier exons: on a l'union des exons de tous les transcripts...
CLOSED: [2023-02-19 Sun 12:05]

Replacement in projects/bisonex.org at line 2941 [5.35]

B:BD[2.9019] → [2.9019:9286]

∅:D[2.9286] → [4.4738:4756]

B:BD[6.891] → [4.4738:4756]

∅:D[4.4756] → [3.1628:2032]

B:BD[3.1628] → [3.1628:2032]

******* Erreur dans le paramère : -f au lieu de -R !!
Il faut supprimer les overlap (et trier avant)
 bedtools sort -i illumina_exons.bed > illumina_exons.bed.sorted
 bedtools merge -i illumina_exons.bed.sorted > HG001_GRCh38_1_22_v4.2.1_benchmark_illumina_exons.be
******* rtg tools
Threshold  True-pos-baseline  True-pos-call  False-pos  False-neg  Precision  Sensitivity  F-measure
----------------------------------------------------------------------------------------------------
    3.000               1015            910        206      32531     0.8154       0.0303     0.0583
     None               1015            910        206      32531     0.8154       0.0303     0.0583

[2.9019]

[7.818]

******* TODO Bed illumina
******** KILL Sans filtre vep: Inversion truth et query... on recommence
CLOSED: [2023-02-19 Sun 13:15]
******** TODO Sans filtre vep: mieux mais pas exceptionnel
cd work/00/2c72e62400956c96fb101ac7af405e/
$ cat .command.out
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision
INDEL    ALL          922       490       432          942       439          0     32     56       0.531453          0.533970
INDEL   PASS          922       490       432          942       439          0     32     56       0.531453          0.533970
  SNP    ALL        24618     18689      5929        21257      2571          0    239     17       0.759160          0.879052
  SNP   PASS        24618     18689      5929        21257      2571          0    239     17       0.759160          0.879052
 METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
            0.0         0.532709                     NaN                     NaN                   1.628743                   2.799180
            0.0         0.532709                     NaN                     NaN                   1.628743                   2.799180
            0.0         0.814719                2.899604                2.881526                   1.598479                   1.564378
            0.0         0.814719                2.899604                2.881526                   1.598479                   1.564378
******** TODO Comprendre pour les FN explosent avec vep annot