Sam’s Notebook:FastQC – RRBS Geoduck BS-seq FASTQ data

0000-0002-2747-368X

Earlier today I finished trimming Hollie’s RRBS BS-seq FastQ data.

However, the original files were never analyzed with FastQC, so I ran it on the original files.

These libraries were originally created by Hollie Putnam using the TruSeq DNA Methylation Kit (Illumina):

FastQC was run, followed by MultiQC. Analysis was run on Roadrunner.

All analysis is documented in a Jupyter Notebook; see link below.

Jupyter Notebook:

Sam’s Notebook:TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data

0000-0002-2747-368X

Steven requested that I trim the Geoduck RRBS libraries that we have, in preparation to run them through Bismark.

These libraries were originally created by Hollie Putnam using the TruSeq DNA Methylation Kit (Illumina):

All analysis is documented in a Jupyter Notebook; see link below.

Overview of process:

  1. Copy EPI* FastQ files from owl/P_generosa to roadrunner.
  2. Confirm data integrity via MD5 checksums.
  3. Run TrimGalore! with --paired, --rrbs, and --non-directional settings.
  4. Run FastQC and MultiQC on trimmed files.
  5. Copy all data to owl (see Results below for link).
  6. Confirm data integrity via MD5 checksums.

Jupyter Notebook:

Sam’s Notebook:Data Management – Illumina NovaSeq Geoduck Genome Sequencing

0000-0002-2747-368X

As part of the Illumina collaborative geoduck genome sequencing project, their end goal has always been to sequence the genome in a single run.

They’ve finally attempted this by running 10x Genomics, Hi-C, Nextera, and TruSeq libraries in a single run of the NovaSeq.

I downloaded the data using the BaseSpace downloader using Chrome on a Windows 7 computer (this is not available on Ubuntu and the command line tools that are available from Illumina are too confusing for me to bother spending the time on to figure out how to use them just to download the data).

Data was saved here:

Generated MD5 checksums (using md5sum on Ubuntu) and appended to the checksums file:

Illumina was unable to provide MD5 checksums on their end, so I was unable to confirm data integrity post-download.

Illumina sample info is here:

Will add info to:

List of files received:

 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L001_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L001_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleA_S10_L002_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L001_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L001_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L002_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleB_S11_L002_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L001_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L001_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L002_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleC_S12_L002_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L001_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L001_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L002_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x5-A3-MultipleD_S13_L002_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L001_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L001_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L002_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleA_S14_L002_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L001_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L001_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L002_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleB_S15_L002_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L001_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L001_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L002_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleC_S16_L002_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L001_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L001_R2_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L002_R1_001.fastq.gz 10x-Genomics-Libraries-Geo10x6-B3-MultipleD_S17_L002_R2_001.fastq.gz HiC-Libraries-GeoHiC-C3-N701_S18_L001_R1_001.fastq.gz HiC-Libraries-GeoHiC-C3-N701_S18_L001_R2_001.fastq.gz HiC-Libraries-GeoHiC-C3-N701_S18_L002_R1_001.fastq.gz HiC-Libraries-GeoHiC-C3-N701_S18_L002_R2_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP10-B2-AD013_S7_L001_R1_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP10-B2-AD013_S7_L001_R2_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP10-B2-AD013_S7_L002_R1_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP10-B2-AD013_S7_L002_R2_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP11-C2-AD014_S8_L001_R1_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP11-C2-AD014_S8_L001_R2_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP11-C2-AD014_S8_L002_R1_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP11-C2-AD014_S8_L002_R2_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP12-D2-AD015_S9_L001_R1_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP12-D2-AD015_S9_L001_R2_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP12-D2-AD015_S9_L002_R1_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP12-D2-AD015_S9_L002_R2_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP9-A2-AD002_S6_L001_R1_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP9-A2-AD002_S6_L001_R2_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP9-A2-AD002_S6_L002_R1_001.fastq.gz Nextera-Mate-Pair-Library-GeoNMP9-A2-AD002_S6_L002_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L001_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L001_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L002_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L002_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L001_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L001_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L002_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L002_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L001_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L001_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L002_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L002_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L001_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L001_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L002_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L002_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L001_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L001_R2_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L002_R1_001.fastq.gz Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L002_R2_001.fastq.gz 

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