In [1]:

    

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


    

In [3]:

    

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


    

    




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

In [4]:

    

!ls -lh


    

    




total 5392464
-rw-rw-rw-  1 Steven  staff   8.9M Oct 17 12:06 1_ATCACG_L001_R1_001.fastq.gz
-rw-rw-rw-  1 Steven  staff   638M Oct 17 12:14 2_CGATGT_L001_R1_001.fastq.gz
-rw-rw-rw-  1 Steven  staff   633M Oct 17 12:20 3_TTAGGC_L001_R1_001.fastq.gz
-rw-rw-rw-  1 Steven  staff   671M Oct 17 12:25 5_ACAGTG_L001_R1_001.fastq.gz
-rw-rw-rw-  1 Steven  staff   667M Oct 17 12:29 6_GCCAAT_L001_R1_001.fastq.gz
-rw-rw-rw-  1 Steven  staff    15M Oct 17 12:29 7_CAGATC_L001_R1_001.fastq.gz

In [5]:

    

!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  548M  100  548M    0     0  23.6M      0  0:00:23  0:00:23 --:--:-- 25.9M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  764M  100  764M    0     0  13.2M      0  0:00:57  0:00:57 --:--:-- 17.5M

In [3]:

    

# Genome


    

In [3]:

    

cd ../data


    

    




/Volumes/caviar/wd/data

In [ ]:

    

!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  14.3M      0  0:00:53  0:00:53 --:--:-- 15.5M

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


    

In [ ]:

    

#check to se if SE