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Assess Oly Methylation datasets #225

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sr320 opened this Issue Apr 25, 2018 · 8 comments

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sr320 commented Apr 25, 2018

Using Bismark / or related nextflow pipeline...

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sr320 commented Apr 25, 2018

note I have some files @ /gscratch/srlab/sr320/data/olurida-bs

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kubu4 commented Apr 25, 2018

What do you mean by "assess"?

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sr320 commented Apr 25, 2018

Analyze.. determine differences in methylation across samples...

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kubu4 commented May 8, 2018

Edited to add notebook link:

http://onsnetwork.org/kubu4/2018/05/08/bs-seq-mapping-olympia-oyster-bisulfite-sequencing-trimgalore-fastqc-bismark/

Summary (notebook entry is forthcoming):

Ran TrimGalore on all seqs prior to Bismark.

Bismark default settings, plus:

  • -u 1000000
  • --non-directional

Genome (JPG): pbjelly assembly

Might be worth re-running using assembly with fewer Ns.


Whole genome BS-seq (2015)

Prep overview
  • Library prep: Roberts Lab
  • Sequencing: Genewiz
Bismark Report Mapping Percentage
1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 40.3%
2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 39.9%
3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 40.2%
4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 40.4%
5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 39.9%
6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 39.6%
7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 39.9%
8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 39.7%

MBD BS-seq (2015)

Prep overview
  • MBD: Roberts Lab
  • Library prep: ZymoResearch
  • Sequencing: ZymoResearch
Bismark Report Mapping Percentage
zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt 33.0%
zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt 34.1%
zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt 32.5%
zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt 32.8%
zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt 35.2%
zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt 35.5%
zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt 32.8%
zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt 33.0%
zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt 34.7%
zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt 34.9%
zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt 30.5%
zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt 35.8%
zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt 32.5%
zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt 30.8%
zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt 31.3%
zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt 30.7%
zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt 32.4%
zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt 34.9%
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sr320 commented May 19, 2018

this would go to Methylkit to check for differences ...

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kubu4 commented Aug 16, 2018

Full Bismark pipeline run on full data sets:

http://onsnetwork.org/kubu4/2018/08/16/dna-methylation-analysis-bismark-pipeline-on-all-olympia-oyster-bsseq-datasets/

Will start looking at data based on the two different experiments in MethylKit.

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kubu4 commented Sep 4, 2018

Discussed with Steven last week. Will re-trim (just 10bp 5' end of reads), and change Bismark cutoff score. Jobs are queued on Mox (which is down for maintenance through 9/11/2018).

Then, will process with MethylKit and test out various coverage cutoff values.

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kubu4 commented Sep 18, 2018

@sr320 sr320 closed this Sep 25, 2018

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