Posted by & filed under Ostrea lurida.

 

BS-seq_Libraries_for_Sequencing_at_Genewiz___Sam_s_Notebook_1C505006.png

For the 12 samples

Select 4 samples from 1NF gel take 2
Select 4 samples from 2NF gel take 2

Select 2 from gel take 2 Lotterhos
M1
M2
M3

Select 2 from the following sent to Katie (do not have to run on gel)
NF2 14
NF2 6
NF2 18
NF2 15
NF2 17

DNA_Isolation_–_Oly_gDNA_for_BS-seq___Sam_s_Notebook_1C50508C.png

Short term will just check out the first 8.

These are samples outplanted at Oyster Bay and Fidalgo, and in both cases parents from Fidalgo.

The hypothesis is that Epigenetic pattern will differ (and we can attribute to Environment)

Quick look at raw data

BS-seq_Libraries_for_Sequencing_at_Genewiz___Sam_s_Notebook_1C505191.png
Sequencing Platform: Illumina HiSeq2500

Read Type/Length: 50bp single-end, single index

Total Number of Reads: 116,280,817

Reads Per File:

11_GGCTAC_L001_R1_001.fastq.gz    10933121

12_CTTGTA_L001_R1_001.fastq.gz    10816647

1_ATCACG_L001_R1_001.fastq.gz    9402890

2_CGATGT_L001_R1_001.fastq.gz    11954873

3_TTAGGC_L001_R1_001.fastq.gz    11817358

4_TGACCA_L001_R1_001.fastq.gz    11606618

5_ACAGTG_L001_R1_001.fastq.gz    12589609

6_GCCAAT_L001_R1_001.fastq.gz    12489766

7_CAGATC_L001_R1_001.fastq.gz    10295293

8_ACTTGA_L001_R1_001.fastq.gz    14374642

Unzip

In [1]:
cd /Volumes/Histidine/hectocotylus/whole-BS-01
/Volumes/Histidine/hectocotylus/whole-BS-01
In [2]:
%%bash
for f in *.gz
do
  STEM=$(basename "${f}" .gz)
  gunzip -c "${f}" > /Volumes/Histidine/hectocotylus/whole-BS-01/fq/"${STEM}"
done

FastQC

In [3]:
!/Applications/bioinfo/FastQC/fastqc \
-o /Volumes/Histidine/hectocotylus/whole-BS-01/fq/ \
-t 4 \
/Volumes/Histidine/hectocotylus/whole-BS-01/fq/*
Started analysis of 1_ATCACG_L001_R1_001.fastq
Started analysis of 2_CGATGT_L001_R1_001.fastq
Started analysis of 3_TTAGGC_L001_R1_001.fastq
...
8_ACTTGA_L001_R1_001_fastq_FastQC_Report_1C50546C.png

this unusual pattern seem to hold true..

In [ ]:

 

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