notebook.community

Edit and run



In [1]:

    
bsmaploc="/Users/Shared/Apps/bsmap-2.74/"



In [ ]:

    
cd /Volumes/web-1/halfshell/working-directory/16-10-17



In [2]:

    
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/1_ATCACG_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/2_CGATGT_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/3_TTAGGC_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/5_ACAGTG_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/6_GCCAAT_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/7_CAGATC_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/8_ACTTGA_L001_R1_001.fastq.gz









    



  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  502M  100  502M    0     0  40.3M      0  0:00:12  0:00:12 --:--:-- 75.3M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  637M  100  637M    0     0  73.3M      0  0:00:08  0:00:08 --:--:-- 73.9M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  633M  100  633M    0     0  41.1M      0  0:00:15  0:00:15 --:--:-- 68.8M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  671M  100  671M    0     0  52.8M      0  0:00:12  0:00:12 --:--:-- 75.2M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  667M  100  667M    0     0  42.3M      0  0:00:15  0:00:15 --:--:-- 70.0M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  548M  100  548M    0     0  68.7M      0  0:00:07  0:00:07 --:--:-- 79.7M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  764M  100  764M    0     0  34.5M      0  0:00:22  0:00:22 --:--:-- 69.6M



In [3]:

    
# Genome



In [3]:

    
cd ../data









    



/Volumes/caviar/wd/data



In [5]:

    
!curl -O http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/Ostrea_lurida.scafSeq









    



  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  761M  100  761M    0     0  49.3M      0  0:00:15  0:00:15 --:--:-- 66.0M



In [6]:

    
!md5 /Volumes/caviar/wd/data/O*









    



MD5 (/Volumes/caviar/wd/data/Ostrea_lurida.scafSeq) = f0a7772d4f1074698b50c913783c6fe2



In [8]:

    
!curl http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/md5.txt | grep scaf









    



  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   913  100   913    0     0   8304      0 --:--:-- --:--:-- --:--:--  8376
f0a7772d4f1074698b50c913783c6fe2  Assembly_Result/Ostrea_lurida.scafSeq



In [4]:

    
ls ../









    



2016-10-11/ data/



In [4]:

    
cd ../2016-10-11/









    



/Volumes/caviar/wd/2016-10-11



In [5]:

    
ls









    



10_TAGCTT_L001_R1_001.fastq.gz  bsmap_out_M3.sam
1_ATCACG_L001_R1_001.fastq.gz   methratio_out_M2.txt
2_CGATGT_L001_R1_001.fastq.gz   methratio_out_M2CG.txt
3_TTAGGC_L001_R1_001.fastq.gz   methratio_out_M2CGi.txt
4_TGACCA_L001_R1_001.fastq.gz   methratio_out_M3.txt
5_ACAGTG_L001_R1_001.fastq.gz   methratio_out_M3CG.txt
6_GCCAAT_L001_R1_001.fastq.gz   methratio_out_M3CGi.txt
7_CAGATC_L001_R1_001.fastq.gz   mkfmt_M2.txt
8_ACTTGA_L001_R1_001.fastq.gz   mkfmt_M3.txt
9_GATCAG_L001_R1_001.fastq.gz   mkfmti_M2.txt
M2.fastq.gz                     mkfmti_M3.txt
M3.fastq.gz                     mr3x.M1.txt
bsmap_out_1_ATCACG.sam          mr3x.M2.txt
bsmap_out_2_CGATGT.sam          mr3x.M3.txt
bsmap_out_3_TTAGGC.sam          mr3xi.M2.txt
bsmap_out_4_TGACCA.sam          mr3xi.M3.txt
bsmap_out_M2.sam



In [12]:

    
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/4_TGACCA_L001_R1_001.fastq.gz









    



  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  619M  100  619M    0     0  51.2M      0  0:00:12  0:00:12 --:--:-- 32.3M



In [ ]:

    
for i in ("1_ATCACG","2_CGATGT","3_TTAGGC","4_TGACCA","5_ACAGTG","6_GCCAAT","7_CAGATC","8_ACTTGA"):
    !{bsmaploc}bsmap \
-a {i}_L001_R1_001.fastq.gz \
-d /Volumes/caviar/wd/data/Ostrea_lurida.scafSeq \
-o bsmap_out_{i}.sam \
-p 7









    



BSMAP v2.74
Start at:  Fri Oct 14 06:51:47 2016

Input reference file: /Volumes/caviar/wd/data/Ostrea_lurida.scafSeq 	(format: FASTA)
Load in 765755 db seqs, total size 776306190 bp. 11 secs passed
total_kmers: 43046721



In [ ]:

    
for i in ("4_TGACCA","5_ACAGTG","6_GCCAAT","7_CAGATC","8_ACTTGA"):
    !{bsmaploc}bsmap \
-a {i}_L001_R1_001.fastq.gz \
-d /Volumes/caviar/wd/data/Ostrea_lurida.scafSeq \
-o bsmap_out_{i}.sam \
-p 4 \
2> bsmap_out_{i}.stderr



In [ ]:

    
#check to se if SE