Olympia Oyster Genome Read Check

Reposted from the FISH546 Project

I inadvertently started with ducks but now have rebooted with the Olympia oyster genome. The first step will be just seeing what we have..

What we expected
project-olympia_oyster-genomic_contract_BGI_Olurida_denovo_F15FTSUSAT0327_pdf_at_master_·_RobertsLab_project-olympia_oyster-genomic_1DB64532.png

Received: 20160127

Format: FASTQ (Illumina HiSeq4000)

Location: http://owl.fish.washington.edu/nightingales/O_lurida/

Files:

FILENAME READS INSERT SIZE SEQUENCING
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz 61253141 500bp PE150
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz 61253141 500bp PE150
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz 58755925 800bp PE150
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz 53307837 800bp PE150
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz 27731148 300bp PE150
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz 43938762 300bp PE150
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz 87198584 5000bp PE50
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz 87198584 5000bp PE50
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz 43766527 10000bp PE50
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz 43766527 10000bp PE50
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz 87135961 5000bp PE50
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz 87135961 5000bp PE50
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz 43138844 10000bp PE50
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz 43138844 10000bp PE50
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz 95270180 2000bp PE50
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz 95270180 2000bp PE50
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz 92524416 2000bp PE50
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz 92524416 2000bp PE50
Data: Initial genome assembly

Received: 20160314

Formats: TXT, FASTA

Location: http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160314/

Files:

FILENAME DESCRIPTION
md5.txt Checksum file to verify integrity of files after downloading.
N50.txt Contains limited stats on scaffolds provided.
scaffold.fa.fill A FASTA file of scaffolds. 
max_length: 13711
N90	118	11683060
N80	127	9895195
N70	137	8233707
N60	150	6700118
N50	150	5237787
N40	150	3775455
N30	150	2313124
N20	209	964091
N10	494	234061
Total length: 2193496679
number>100bp	13627636
number>2000bp	13480
Data: Initial small insert library genome assembly

Received: 20160512

Formats: TXT, FASTA, PDF, PNG, FASTQ

Location: http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/

Files:

FASTQ Files

FILENAME READS
51114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz.clean.dup.clean.gz 61253141
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz.clean.dup.clean.gz 61253141
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz.clean.dup.clean.gz 58755925
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz 58755925
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz 43938762
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz.clean.dup.clean.gz 43938762

May 2016 Report 20160512_F15FTSUSAT0327_genome_survey_pdf_1DB646E9.png

20160512_F15FTSUSAT0327_genome_survey_pdf_1DB64928.png

FastQC

$ ls nightingales/O_lurida/*I1*
nightingales/O_lurida/151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz*
nightingales/O_lurida/151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz*
nightingales/O_lurida/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz*
nightingales/O_lurida/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz*
nightingales/O_lurida/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz*
nightingales/O_lurida/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz*
nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz*

!/Applications/bioinfo/FastQC/fastqc \
nightingales/O_lurida/*I1* \
-t 6 \
-o /Users/sr320/git-repos/student-fish546-2016/analyses/

!ls /Users/sr320/git-repos/student-fish546-2016/analyses/
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq_fastqc.html
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq_fastqc.zip
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq_fastqc.html
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq_fastqc.zip
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq_fastqc.html
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq_fastqc.zip
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq_fastqc.html
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq_fastqc.zip
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq_fastqc.html
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq_fastqc.zip

Seemed to have missed a few.. 66,96

MultiQC

Full Report:
http://owl.fish.washington.edu/halfshell/working-directory/16-10-19/multiqc_report.html#

!multiqc /Users/sr320/git-repos/student-fish546-2016/analyses

MultiQC_Report_1DB7BD6C.png

MultiQC_Report_1DB7BDB3.png

MultiQC_Report_1DB7BDEE.png

Written on October 19, 2016