B:BD[
2.32799] → [
2.32799:36464]
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN
--------------------------------------------------------------------------------------------------------------
browser details YourSeq 124 1 128 128 98.5% chr15_ML143370v1_fix + 172243 172370 128 What is chrom_fix?
browser details YourSeq 124 1 128 128 98.5% chr15 + 74342974 74343101 128
browser details YourSeq 23 1 25 128 96.0% chr19 - 33396097 33396121 25
Second
--------------------------------------------------------------------------------------------------------------
browser details YourSeq 126 1 128 128 99.3% chr15_ML143370v1_fix - 172243 172370 128 What is chrom_fix?
browser details YourSeq 126 1 128 128 99.3% chr15 - 74342974 74343101 128
browser details YourSeq 23 104 128 128 96.0% chr19 + 33396097 33396121 25
******* DONE Bwa mem à la main GRCh38.p13 : on est dans une zone NW
CLOSED: [2023-06-04 Sun 21:51]
On met les 2 reads dans des fichiers séparés puis
#+begin_src sh
cd /Work/Users/apraga/bisonex/tests/xamscissors/align
bwa mem /Work/Groups/bisonex/data/genome/GRCh38.p13/bwa/genomeRef test1.fq test2.fq
#+end_src
A00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;
******* DONE GRCh38.p14: idem
CLOSED: [2023-06-04 Sun 21:51]
A00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;
******* DONE GRCh38 : ok
CLOSED: [2023-06-04 Sun 22:15]
bwa mem /Work/Projects/bisonex/data/genome/GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna test1.fq test2.fq
****** DONE Vérifier que les reads ont la même qualité sur les fichiers d'origine: oui
CLOSED: [2023-06-04 Sun 21:07]
****** TODO Supprimer les NW_ ?
SCHEDULED: <2023-06-04 Sun>
Attente réponse alexis
**** TODO Test Indel
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN
--------------------------------------------------------------------------------------------------------------
browser details YourSeq 124 1 128 128 98.5% chr15_ML143370v1_fix + 172243 172370 128 What is chrom_fix?
browser details YourSeq 124 1 128 128 98.5% chr15 + 74342974 74343101 128
browser details YourSeq 23 1 25 128 96.0% chr19 - 33396097 33396121 25
Second
--------------------------------------------------------------------------------------------------------------
browser details YourSeq 126 1 128 128 99.3% chr15_ML143370v1_fix - 172243 172370 128 What is chrom_fix?
browser details YourSeq 126 1 128 128 99.3% chr15 - 74342974 74343101 128
browser details YourSeq 23 104 128 128 96.0% chr19 + 33396097 33396121 25
******* DONE Bwa mem à la main GRCh38.p13 : on est dans une zone NW
CLOSED: [2023-06-04 Sun 21:51]
On met les 2 reads dans des fichiers séparés puis
#+begin_src sh
cd /Work/Users/apraga/bisonex/tests/xamscissors/align
bwa mem /Work/Groups/bisonex/data/genome/GRCh38.p13/bwa/genomeRef test1.fq test2.fq
#+end_src
A00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;
******* DONE GRCh38.p14: idem
CLOSED: [2023-06-04 Sun 21:51]
A00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;
******* DONE GRCh38 : ok
CLOSED: [2023-06-04 Sun 22:15]
bwa mem /Work/Projects/bisonex/data/genome/GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna test1.fq test2.fq
****** DONE Vérifier que les reads ont la même qualité sur les fichiers d'origine: oui
CLOSED: [2023-06-04 Sun 21:07]
****** DONE Supprimer les NW_ geonem conti : 568/590
CLOSED: [2023-06-06 Tue 22:37] SCHEDULED: <2023-06-04 Sun>
Toujours mapping quality = 0
****** DONE Tester sur chr6 32,040,110: aligne sur NT_
CLOSED: [2023-06-06 Tue 22:37]
Comprendre A00853:477:HMLWYDSX3:3:2114:14742:8860
zgrep -A 3 "A00853:477:HMLWYDSX3:3:2114:14742:8860" *.fq.gz
@A00853:477:HMLWYDSX3:3:2114:14742:8860
CAGGCCAGCCGCTCAGCCCGCTCCTTTCACCCTCTGCAGGAGAGCCTCGTGGCAGGCCAGTGGAGGGACATGATGGACTACATGCTCCAAGGGGTGGCGCAGCCGAGCATGGAAGAGGGCTCTGGACAGCTCCTGGAAGGGCACTTGCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00853:477:HMLWYDSX3:3:2114:14742:8860
CTTTTGCTTGTCCCCAGGACGCACCTCAGGGTGGTGAAGCAAAAAAACCACGGCCCAGGAGAGGGTGGGTGCTGTGGTCTCAGTGCCACCGATCAGGAGGTCCACTGCAGCCATGTGCAAGTGCCCTTCCAGGAGCTGTCCAGAGCCCTCT
+
FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFF,FFFFFFFFFFFF:F:FFFF:FFFFF,,FFF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFFFFF:FFFF,F:FFFFF:FFFFFFFFF:FFFF,FFFFFFFFF
****** TODO Supprimer NW_ et NT_
**** TODO Test Indel
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]