notebook.community

Edit and run



In [2]:

    
! ls









    



00_fastq_QC.ipynb  learning_phyton.ipynb



In [3]:

    
! pwd









    



/home/student/Notebooks/Nazaret



In [4]:

    
! head /media/storage/FASTQs/K562_HindIII_1.fastq









    



@NS500645:59:HCL32BGXY:1:11101:14163:1054 1:N:0:GCCAAT
CATTCNTAAAGAAAAGAATTTTCAACNCAGAATTTCATATCCAGCCAACTAAGCTAGCTTCAAGGAAATACATTT
+
AAAAA#EEAEEEEEEEEEEAE/EEEE#EEEEEEEEEEEEEEEEAE</EE/EEEEAEEEEEEEEEEEAAEE</EEE
@NS500645:59:HCL32BGXY:1:11101:4416:1054 1:N:0:GCCAAT
CGAGTNAGGGAAGCTAGCTTCCATTCNTTTGCTTCTGTTGTGTGTTTTTTCTTTTGTTTTTTTTTTGTTTTGGTT
+
AAAAA#EEEEEEEEEEEEEEAEEEE/#EEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEE/<EEEEEAE
@NS500645:59:HCL32BGXY:1:11101:14193:1055 1:N:0:GCCAAT
AAAGTNCCCTGCATGATAGCATTTGTATAAAGTTCAAAACAGACCAAATGGATCTCTAATTTGTAGAAGGTCAGG



In [5]:

    
! wc -l /media/storage/FASTQs/K562_HindIII_1.fastq









    



40000000 /media/storage/FASTQs/K562_HindIII_1.fastq

FASTQ quality check using TADbit



In [8]:

    
from pytadbit.utils.fastq_utils import quality_plot



In [ ]:

    
quality_plot("/media/storage/FASTQs/K562_HindIII_1.fastq", r_enz="HindIII", nreads=1000000)

PHRED score >25 is ok

Number of ends >5% is bad



In [14]:

    
quality_plot("/media/storage/FASTQs/K562_HindIII_1.fastq", r_enz="HindIII", nreads=1000000)









    












    Out[14]:





(0.8355, 28.7747)



In [16]:

    
quality_plot("/media/storage/FASTQs/K562_MboI_1.fastq", r_enz="MboI", nreads=1000000)









    












    Out[16]:





(2.7736, 35.1285)

Out[-]: (%dangling ends, %ligation sites)



In [19]:

    
quality_plot("/media/storage/FASTQs/K562_MboI_2.fastq", r_enz="MboI", nreads=100000)









    












    Out[19]:





(2.662, 33.142)



In [ ]: