00_fastq_QC



In [2]:

    
¡ ls









    



  File "<ipython-input-2-b59d2317c62a>", line 1
    ¡ ls
    ^
SyntaxError: invalid syntax



In [3]:

    
¡ ls









    



  File "<ipython-input-3-b59d2317c62a>", line 1
    ¡ ls
    ^
SyntaxError: invalid syntax



In [4]:

    
! ls









    



00_fast_QC.ipynb  learning_python.ipynb



In [5]:

    
! head/media/storage/FASTQs/









    



/bin/sh: 1: head/media/storage/FASTQs/: not found



In [6]:

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









    



/bin/sh: 1: head/media/storage/FASTQs/K562_HindIII_1.fastq: not found



In [7]:

    
! 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 [10]:

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









    



40000000 /media/storage/FASTQs/K562_HindIII_1.fastq

FASTQ quality check using TADbit



In [12]:

    
from pytadbit.utils.fastq_utils import quality_plot



In [14]:

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









    












    Out[14]:





(0.8117, 27.4062)



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