Geoduck-EPI on Hi-C Draft
As a better assembly is coming online for the Geoduck, we have started to look at Bismark mapping of prior samples.
For a refresh there are 50 samples (or 53)
I did a run on mox
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0505
source /gscratch/srlab/programs/scripts/paths.sh
find /gscratch/srlab/sr320/data/0504/EPI-*R1* \
| xargs basename -s _L005_R1_001.fastq.gz | xargs -I{} /gscratch/srlab/programs/Bismark-0.19.0/bismark \
--path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 \
-p 28 \
-multicore 4 \
/gscratch/srlab/sr320/data/hi-c \
-1 /gscratch/srlab/sr320/data/0504/{}_L005_R1_001.fastq.gz \
-2 /gscratch/srlab/sr320/data/0504/{}_L005_R2_001.fastq.gz
About 17 completed
0505/EPI-103_S27_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 28.6%
0505/EPI-104_S28_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 27.8%
0505/EPI-111_S29_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 27.6%
0505/EPI-113_S30_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 27.8%
0505/EPI-119_S31_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 27.9%
0505/EPI-120_S32_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 29.2%
0505/EPI-127_S33_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 29.3%
0505/EPI-128_S34_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 28.9%
0505/EPI-135_S35_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 25.4%
0505/EPI-135WG_S42_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 26.8%
0505/EPI-136_S36_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 25.1%
0505/EPI-143_S37_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 27.4%
0505/EPI-145_S38_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 28.3%
0505/EPI-41_S38_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 19.5%
0505/EPI-42_S39_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 22.2%
0505/EPI-43_S40_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 17.5%
0505/EPI-44_S41_L005_R1_001_bismark_bt2_PE_report.txt:Mapping efficiency: 7.9%
Not clear if this was a system error or not, thus running a -u 10000 to see if I can get all samples processed.
In fact it appears there is an error. Again it stops at 44.
Now realizing issue in basename (hint):
-rw-rw-rw- 1 sr320 hyak-coenv 1.2G Dec 28 2016 EPI-103_S27_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.2G Dec 28 2016 EPI-103_S27_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.7G Dec 28 2016 EPI-104_S28_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.7G Dec 28 2016 EPI-104_S28_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.6G Dec 28 2016 EPI-111_S29_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.5G Dec 28 2016 EPI-111_S29_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.5G Dec 28 2016 EPI-113_S30_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.5G Dec 28 2016 EPI-113_S30_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.7G Dec 28 2016 EPI-119_S31_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.7G Dec 28 2016 EPI-119_S31_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.4G Dec 28 2016 EPI-120_S32_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.4G Dec 28 2016 EPI-120_S32_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.3G Dec 28 2016 EPI-127_S33_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.3G Dec 28 2016 EPI-127_S33_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.4G Dec 28 2016 EPI-128_S34_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.4G Dec 28 2016 EPI-128_S34_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.6G Dec 28 2016 EPI-135_S35_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.7G Dec 28 2016 EPI-135_S35_L005_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 10G Jan 11 2017 EPI-135WG_S42_L005_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 10G Jan 12 2017 EPI-135WG_S42_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.6G Dec 28 2016 EPI-136_S36_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.6G Dec 28 2016 EPI-136_S36_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.3G Dec 28 2016 EPI-143_S37_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.3G Dec 28 2016 EPI-143_S37_L005_R2_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.5G Dec 28 2016 EPI-145_S38_L005_R1_001.fastq.gz
-rw-rw-rw- 1 sr320 hyak-coenv 1.5G Dec 28 2016 EPI-145_S38_L005_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.6G Jan 11 2017 EPI-151_S2_L002_R1_001.fastq.gz
-rwxrwxr-x 1 sr320 hyak-coenv 1.7G Feb 1 2017 EPI-151_S2_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.7G Jan 11 2017 EPI-152_S3_L002_R1_001.fastq.gz
-rwxrwxr-x 1 sr320 hyak-coenv 1.7G Feb 1 2017 EPI-152_S3_L002_R2_001.fastq.gz
-rwxrwxr-x 1 sr320 hyak-coenv 1.7G Feb 1 2017 EPI-153_S4_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.8G Jan 11 2017 EPI-153_S4_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.5G Jan 11 2017 EPI-154_S5_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.5G Jan 11 2017 EPI-154_S5_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 889M Jan 11 2017 EPI-159_S6_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 920M Jan 11 2017 EPI-159_S6_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.9G Jan 11 2017 EPI-160_S7_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.9G Jan 11 2017 EPI-160_S7_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.4G Jan 11 2017 EPI-161_S8_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.4G Jan 11 2017 EPI-161_S8_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.3G Jan 11 2017 EPI-162_S9_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.3G Jan 11 2017 EPI-162_S9_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.4G Jan 11 2017 EPI-167_S10_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.4G Jan 11 2017 EPI-167_S10_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.3G Jan 11 2017 EPI-168_S11_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.3G Jan 11 2017 EPI-168_S11_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.2G Jan 11 2017 EPI-169_S12_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.3G Jan 11 2017 EPI-169_S12_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.5G Jan 11 2017 EPI-170_S13_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.6G Jan 11 2017 EPI-170_S13_L002_R2_001.fastq.gz
-rwxrwxr-x 1 sr320 hyak-coenv 1.4G Feb 1 2017 EPI-175_S14_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.4G Jan 11 2017 EPI-175_S14_L003_R2_001.fastq.gz
-rwxrwxr-x 1 sr320 hyak-coenv 2.0G Feb 1 2017 EPI-176_S15_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 2.1G Jan 11 2017 EPI-176_S15_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.6G Jan 11 2017 EPI-181_S16_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.6G Jan 11 2017 EPI-181_S16_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.8G Jan 11 2017 EPI-182_S17_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.8G Jan 11 2017 EPI-182_S17_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.2G Jan 11 2017 EPI-184_S18_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.2G Jan 11 2017 EPI-184_S18_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 643M Jan 11 2017 EPI-185_S19_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 648M Jan 11 2017 EPI-185_S19_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.5G Jan 11 2017 EPI-187_S20_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.5G Jan 11 2017 EPI-187_S20_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.3G Jan 11 2017 EPI-188_S21_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.4G Jan 11 2017 EPI-188_S21_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.8G Jan 11 2017 EPI-193_S22_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.9G Jan 11 2017 EPI-193_S22_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.6G Jan 11 2017 EPI-194_S23_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.6G Jan 11 2017 EPI-194_S23_L003_R2_001.fastq.gz
-rwxrwxr-x 1 sr320 hyak-coenv 1002M Feb 1 2017 EPI-199_S24_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.1G Jan 11 2017 EPI-199_S24_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.5G Jan 11 2017 EPI-200_S25_L003_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.6G Jan 11 2017 EPI-200_S25_L003_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.4G Jan 11 2017 EPI-205_S26_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.4G Jan 11 2017 EPI-205_S26_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.8G Jan 11 2017 EPI-206_S27_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.9G Jan 11 2017 EPI-206_S27_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 2.0G Jan 11 2017 EPI-208_S28_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 2.1G Jan 11 2017 EPI-208_S28_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.7G Jan 11 2017 EPI-209_S29_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.7G Jan 11 2017 EPI-209_S29_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.6G Jan 11 2017 EPI-214_S30_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.6G Jan 11 2017 EPI-214_S30_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.3G Jan 11 2017 EPI-215_S31_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.3G Jan 11 2017 EPI-215_S31_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 941M Jan 11 2017 EPI-220_S32_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 960M Jan 11 2017 EPI-220_S32_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.2G Jan 11 2017 EPI-221_S33_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.3G Jan 11 2017 EPI-221_S33_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 624M Jan 11 2017 EPI-226_S34_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 631M Jan 11 2017 EPI-226_S34_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 836M Jan 11 2017 EPI-227_S35_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 852M Jan 11 2017 EPI-227_S35_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.1G Jan 11 2017 EPI-229_S36_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.1G Jan 11 2017 EPI-229_S36_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.7G Jan 11 2017 EPI-230_S37_L004_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.7G Jan 11 2017 EPI-230_S37_L004_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.5G Jan 11 2017 EPI-41_S38_L005_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.5G Jan 11 2017 EPI-41_S38_L005_R2_001.fastq.gz
-rwxrwxr-x 1 sr320 hyak-coenv 1.7G Feb 1 2017 EPI-42_S39_L005_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.8G Jan 11 2017 EPI-42_S39_L005_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.7G Jan 11 2017 EPI-43_S40_L005_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 1.7G Jan 11 2017 EPI-43_S40_L005_R2_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 2.0G Jan 11 2017 EPI-44_S41_L005_R1_001.fastq.gz
-rwxr-xr-x 1 sr320 hyak-coenv 2.3G Jan 11 2017 EPI-44_S41_L005_R2_001.fastq.gz
Rewrite
find /gscratch/srlab/sr320/data/0504/EPI-*R1* \
| xargs basename -s _R1_001.fastq.gz | xargs -I{} /gscratch/srlab/programs/Bismark-0.19.0/bismark \
--path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 \
-p 28 \
-multicore 4 \
-u 10000 \
/gscratch/srlab/sr320/data/hi-c \
-1 /gscratch/srlab/sr320/data/0504/{}_R1_001.fastq.gz \
-2 /gscratch/srlab/sr320/data/0504/{}_R2_001.fastq.gz
This took 7 hours on Mox. Mapping efficiency a little less that 20%.
Will modify min score. --score_min L,0,-0.9
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0512
source /gscratch/srlab/programs/scripts/paths.sh
find /gscratch/srlab/sr320/data/0504/EPI-*R1* \
| xargs basename -s _R1_001.fastq.gz | xargs -I{} /gscratch/srlab/programs/Bismark-0.19.0/bismark \
--path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 \
--score_min L,0,-0.9 \
-p 28 \
-u 10000 \
-multicore 4 \
/gscratch/srlab/sr320/data/hi-c \
-1 /gscratch/srlab/sr320/data/0504/{}_R1_001.fastq.gz \
-2 /gscratch/srlab/sr320/data/0504/{}_R2_001.fastq.gz
Mapping efficiency increased
Mapping efficiency: 59.6%
Mapping efficiency: 58.5%
Mapping efficiency: 57.9%
Mapping efficiency: 58.2%
Mapping efficiency: 57.6%
Mapping efficiency: 59.2%
Mapping efficiency: 59.3%
Mapping efficiency: 58.7%
Mapping efficiency: 54.2%
Mapping efficiency: 56.8%
Mapping efficiency: 54.6%
Mapping efficiency: 56.0%
Mapping efficiency: 57.5%
Mapping efficiency: 43.4%
Mapping efficiency: 50.4%
Mapping efficiency: 42.0%
Mapping efficiency: 48.4%
Mapping efficiency: 51.4%
Mapping efficiency: 42.3%
Mapping efficiency: 41.7%
Mapping efficiency: 41.4%
Mapping efficiency: 55.6%
Mapping efficiency: 51.9%
Mapping efficiency: 46.1%
Mapping efficiency: 42.5%
Mapping efficiency: 52.9%
Mapping efficiency: 49.2%
Mapping efficiency: 53.2%
Mapping efficiency: 53.8%
Mapping efficiency: 49.8%
Mapping efficiency: 48.3%
Mapping efficiency: 47.3%
Mapping efficiency: 39.0%
Mapping efficiency: 37.8%
Mapping efficiency: 55.0%
Mapping efficiency: 41.7%
Mapping efficiency: 42.4%
Mapping efficiency: 26.1%
Mapping efficiency: 27.4%
Mapping efficiency: 31.5%
Mapping efficiency: 49.3%
Mapping efficiency: 46.8%
Mapping efficiency: 42.6%
Mapping efficiency: 45.0%
Mapping efficiency: 32.5%
Mapping efficiency: 52.8%
Mapping efficiency: 43.6%
Mapping efficiency: 47.3%
Mapping efficiency: 40.4%
Mapping efficiency: 45.9%
Mapping efficiency: 50.1%
Mapping efficiency: 39.4%
Mapping efficiency: 17.3%
Then went full fun
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0513
source /gscratch/srlab/programs/scripts/paths.sh
find /gscratch/srlab/sr320/data/0504/EPI-*R1* \
| xargs basename -s _R1_001.fastq.gz | xargs -I{} /gscratch/srlab/programs/Bismark-0.19.0/bismark \
--path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 \
--score_min L,0,-0.9 \
-p 28 \
-multicore 4 \
/gscratch/srlab/sr320/data/hi-c \
-1 /gscratch/srlab/sr320/data/0504/{}_R1_001.fastq.gz \
-2 /gscratch/srlab/sr320/data/0504/{}_R2_001.fastq.gz
It seemed to end
[sr320@mox1 0513]$ cat *.txt | grep "Mapping"
Mapping efficiency: 60.1%
Mapping efficiency: 58.5%
Mapping efficiency: 57.9%
Mapping efficiency: 58.4%
Mapping efficiency: 57.5%
Mapping efficiency: 59.8%
Mapping efficiency: 59.7%
Mapping efficiency: 58.9%
Now running with 30k version of genome
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0515
source /gscratch/srlab/programs/scripts/paths.sh
find /gscratch/srlab/sr320/data/0504/EPI-*R1* \
| xargs basename -s _R1_001.fastq.gz | xargs -I{} /gscratch/srlab/programs/Bismark-0.19.0/bismark \
--path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 \
--score_min L,0,-0.9 \
-p 28 \
-multicore 4 \
/gscratch/srlab/sr320/data/hi-c_30k \
-1 /gscratch/srlab/sr320/data/0504/{}_R1_001.fastq.gz \
-2 /gscratch/srlab/sr320/data/0504/{}_R2_001.fastq.gz
at 05-22-18 it had run 6-21:11:47 with about 33 complete.
UPDATE: 05-25-18- completed. So about 10 days.
output:
http://gannet.fish.washington.edu/seashell/bu-mox/analyses/0515/
Next step
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0525
source /gscratch/srlab/programs/scripts/paths.sh
/gscratch/srlab/programs/Bismark-0.19.0/deduplicate_bismark \
--bam -p \
/gscratch/srlab/sr320/analyses/0515/*.bam
find /gscratch/srlab/sr320/analyses/0525/*deduplicated.bam \
| xargs basename -s _R1_001_bismark_bt2_pe.deduplicated.bam | xargs -I{} /gscratch/srlab/programs/samtools-1.4/samtools \
sort -@ 28 {}_R1_001_bismark_bt2_pe.deduplicated.bam \
-o /gscratch/srlab/sr320/analyses/0525/{}_dedup.sorted.bam
Written on May 10, 2018