<jupyter_start><jupyter_text>Running BSMAP 10k cuttoff | Sample  | Weight (grams in shell)| Length (mm) | Raw 2bRAD reads ||---------|------------------------|-------------|-----------------|| hc1_2B  | 2.2                    |  17.41      | 1521| hc1_4B  | 1.9                    |  20.43           | 2294290| hc2_15B | 2.2                    |  25.33      | 2498| hc2_17  | 1.1                    |  19.38      | (seq 4x)best = 2964986| hc3_1   | 2.2                    |  26.79        | 1863108| hc3_5   | 1.9                    |  19.5       | 1915| hc3_7   | 1.4                    | 18.43            | 2438612| hc3_10  | 1.2                    |  19.80           | 4091281| hc3_11  | 2.1                    |   20.54          | 2901608| ss2_9B  | 1.5                    | 17.2        | 749| ss2_14B | 2.2                    | 21.02       | 29745| ss2_18B | 5.3                    | 35.76       | 3016| ss3_3B  | 2.1                    | 22.71       | 2076769| ss3_14B | 2.4                    | 24.71       | 2661152| ss3_15B | 2.6                    | 26.78       | 2816364| ss3_16B | 4.2                    | 39.57       | 2070520| ss3_20  | 2.3                    | 26.96       | 1656456| ss5_18  | 5.4                    | 27.34       | 2358172<jupyter_code>%%bash
date
system_profiler SPSoftwareDataType
bsmaploc="/Users/Shared/Apps/bsmap-2.74/"

cd /Volumes/web/halfshell/working-directory/
!ls -lh 
mkdir 16-11-23
cd 16-11-23
!ls /Volumes/web/nightingales/O_lurida/20160203_mbdseq/*s456.fastq.gz
!cp /Volumes/web/nightingales/O_lurida/20160203_mbdseq/*s456.fastq.gz /Users/Shared/data/Oly_clambay
pwd
!cp /Users/Steven/Documents/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-10k.fa /Users/Shared/data/Oly_clambay<jupyter_output><empty_output><jupyter_text>for i in ("1","2","3", "4", "5", "6", "7", "8","9", "10", "11","12","13", "14", "15", "16", "17", "18"):    !{bsmaploc}bsmap \-a /Users/Shared/data/Oly_clambay/zr1394_{i}_s456.fastq.gz \-d /Users/Shared/data/Oly_clambay/Ostrea_lurida-Scaff-10k.fa \-o bsmap_out_{i}.sam \-p 8 \2> bsmap_out_{i}.stderr<jupyter_code>!awk '{print $3}' /Volumes/web/halfshell/working-directory/16-11-23/bsmap_out_1.sam | sort -nr \
| grep "s_" > /Users/Shared/data/Oly_clambay/id.txt

for i in ("1","2"):
    !{bsmaploc}bsmap \
-a /Users/Shared/data/Oly_clambay/zr1394_{i}_s456.fastq.gz \
-d /Users/Shared/data/Oly_clambay/Ostrea_lurida-Scaff-10k.fa \
-o /Users/Shared/data/Oly_clambay/bsp_bsmap_out_{i}.bsp \
-p 8 \
2> /Users/Shared/data/Oly_clambay/bsp_bsmap_out_{i}.stderr
!date
!tail *err
for i in ("1_ATCACG","2_CGATGT","3_TTAGGC","5_ACAGTG","4_TGACCA", "6_GCCAAT", "7_CAGATC", "8_ACTTGA"):
    !{bsmaploc}bsmap \
-a ../16-10-17/{i}_L001_R1_001.fastq.gz \
-d Ostrea_lurida-Scaff-10k.fa \
-o bsmap_out_{i}-2.sam \
-p 8 \
2> bsmap_out_{i}-2.stderr
ls -lh bsmap*<jupyter_output>-rw-rw-rw-  1 Steven  staff   411M Oct 29 18:21 bsmap_out_1_ATCACG-2.sam
-rw-rw-rw-  1 Steven  staff    10K Oct 29 18:21 bsmap_out_1_ATCACG-2.stderr
-rw-rw-rw-  1 Steven  staff   8.0M Oct 29 17:16 bsmap_out_1_ATCACG.sam
-rw-rw-rw-  1 Steven  staff   1.0K Oct 29 17:16 bsmap_out_1_ATCACG.stderr
-rw-rw-rw-  1 Steven  staff   513M Oct 29 18:28 bsmap_out_2_CGATGT-2.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 18:28 bsmap_out_2_CGATGT-2.stderr
-rw-rw-rw-  1 Steven  staff   513M Oct 29 17:23 bsmap_out_2_CGATGT.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 17:23 bsmap_out_2_CGATGT.stderr
-rw-rw-rw-  1 Steven  staff   503M Oct 29 18:36 bsmap_out_3_TTAGGC-2.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 18:36 bsmap_out_3_TTAGGC-2.stderr
-rw-rw-rw-  1 Steven  staff   503M Oct 29 17:29 bsmap_out_3_TTAGGC.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 17:29 bsmap_out_3_TTAGGC.stderr
-rw-rw-rw-  1 Steven  staff   512M Oct 29 18:49 bsmap_out_4_TGACCA-2.sam
-rw-rw-rw-  1 Steven  staff    1[...]
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