In [2]:

    

! ls


    

    




00_fastq_QC.ipynb  learning_python.ipynb  test.txt

In [1]:

    

!pwd


    

    




/media/storage/Notebooks2/agnese

In [2]:

    

! 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 [3]:

    

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


    

    




40000000 /media/storage/FASTQs/K562_HindIII_1.fastq

In [8]:

    

from pytadbit.utils.fastq_utils import quality_plot


    

In [9]:

    

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


    

    













    
Out[9]:





(0.8355, 28.7747)

In [10]:

    

quality_plot('/media/storage/FASTQs/K562_HindIII_2.fastq', r_enz='HindIII', nreads=1000000)


    

    













    
Out[10]:





(0.8117, 27.4062)

In [11]:

    

quality_plot('/media/storage/FASTQs/K562_MboI_2.fastq', r_enz='MboI', nreads=1000000)


    

    













    
Out[11]:





(2.774, 33.2535)