[code][sr320@mox2 jobs]$ cat 0809_1500.sh #!/bin/bash...

[sr320@mox2 jobs]$ cat 0809_1500.sh 
#!/bin/bash
## Job Name
#SBATCH --job-name=angsd-05
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=10-100:00:00
## Memory per node
#SBATCH --mem=100G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=sr320@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0809b





source /gscratch/srlab/programs/scripts/paths.sh


/gscratch/srlab/sr320/programs/angsd/angsd -bam /gscratch/srlab/sr320/data/cw/all_bam.bamlist -out Genotypes_parentage2 -GL 1 -doMaf 1 -doMajorMinor 1 -minMaf 0.1 -SNP_pval 1e-6 -minInd 525 -minQ 20 -P 28 -doGeno 2 -doPost 1 -postCutoff 0.95 -doCounts 1 -geno_minDepth 5[sr320@mox2 jobs]$ 

#sbatch

[code][sr320@mox2 jobs]$ cat 0809_1300.sh #!/bin/bash...

[sr320@mox2 jobs]$ cat 0809_1300.sh 
#!/bin/bash
## Job Name
#SBATCH --job-name=angsd-05
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=10-100:00:00
## Memory per node
#SBATCH --mem=100G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=sr320@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0809





source /gscratch/srlab/programs/scripts/paths.sh


/gscratch/srlab/sr320/programs/angsd/angsd \
-bam /gscratch/srlab/sr320/data/cw/all_bam.bamlist \
-out Association_test2 \
-doAsso 1 \
-yBin /gscratch/srlab/sr320/data/cw/YBin_file \
-GL 1 \
-doMaf 1 \
-doMajorMinor 1 \
-minMaf 0.01 \
-SNP_pval 1e-6 \
-minInd 468 \
-minQ 20 \
-doGlf 3 \
-P 28

#sbatch

Sam’s Notebook: Data Received – Geoduck Metagenome HiSeqX Data

0000-0002-2747-368X

Received the data from the geoduck metagenome libraries that I prepared and were sequenced at the Northwest Genomics Center at UW on the HiSeqX (Illumina) – PE 151bp.

FastQ files are being transferred to owl/nightingales/P_generosa.

These aren’t geoduck sequences, but they are part of a geoduck project. Maybe I should establish a metagenomics directory under nightingales?

Will verifiy md5 checksums and update readme file once the transfer is complete.

from Sam’s Notebook https://ift.tt/2OWKinW
via IFTTT

Sam’s Notebook: Genome Annoation – Olympia oyster genome annotation results #02

0000-0002-2747-368X

Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.

See that link for run setup and configuration. They are essentially the same, except for the change I’ll discuss below.

The results from that run can be seen here:

In that previous run, I neglected to provide a transposable elements FastA file for use with RepeatMasker.

I remedied that and re-ran it. I modified maker_opts.ctl to include the following:

 repeat_protein=../../opt/maker/data/te_proteins.fasta #provide a fasta file of transposable element proteins for RepeatRunner 

This TEs file is part of RepeatMasker.

Sam’s Notebook: RNA Isolation & Quantificaiton – Tanner Crab Hemolymph

0000-0002-2747-368X

Isolated RNA from 40 Tanner crab hemolymph samples selected by Grace with the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s protocol, with the following modifications:

  • Added mercaptoethanol (2-ME) to Buffer RLT Plus.
  • All spins were at 21,130g
  • Did not add RNA carrier
  • Used QIAshredder columns to aid in homogenization and removal of insoluble material
  • Eluted with 14uL

RNA was quantified using the Qubit RNA HS (high sensitivity) Assay and run on the Roberts Lab Qubit 3.0.

Used 1uL of sample for quantification.

RNA was returned to the -80C box from where original samples had been stored (Rack 2, Row 3, Column 4).