SEAseq v3.1

Minor Update:

1. Increased memory requested for required tasks (sortbed, macs).
2. Included read length to paired-end bowtie mapping parameters.
3. Corrected FRIP calculation input files
4. Corrected BAM name sort
5. Corrected ROSE input BAMs (now using PCR duplicate removed)
6. Corrected initialization warning from quality metrics script.

What's Changed

• P21 updatemapping by @madetunj in #116
• p23-qcmetrics by @madetunj in #117
• corrected: BAM without PCR duplicates for stitchedpeaks by @madetunj in #120

Full Changelog: 3.0...3.1

SEAseq v3

SEAseq v3.0

Major Update:

• We are happy to introduce PEAseq (Paired-End Antibody Sequencing) pipeline.
• PEAseq performs all analysis provided in SEAseq and also in a paired-end aware manner; results from SEAseq will be stored under /single-end_mode.
• PEAseq scripts are peaseq-case.wdl and peaseq-control.wdl. Execution is similar to SEAseq.

Minor Update:

• Reorganized all coverage files to its dedicated folder /COVERAGE_files
• DNAnexus compatible (using dxWDL)
• Changed color scale to be color-blind friendly

SEAseq v2.4 (and PEAseq v1.0)

SEAseq

Minor Update:

• Reorganized all coverage files to its dedicated folder /COVERAGE_files
• Changed color scale to be color-blind friendly

PEAseq

Initial Release

• PEAseq (Paired-End Antibody sequencing pipeline)
• Performs all analysis provided in SEAseq and also in a paired-end aware manner; results from SEAseq will be stored under /single-end_mode.
• Organizational structure is adopted from SEAseq.

# For sample FASTQs only
java -jar cromwell.jar run peaseq-case.wdl -i inputs.json -o options.json

# For sample FASTQs with Input Control or IgG
java -jar cromwell.jar run peaseq-control.wdl -i inputs.json -o options.json

SEAseq version 2.3

SEAseq version 2.3
Minor Update: migrated container system to GitHub Packages

SEAseq version 2.2

SEAseq version 2.2
Minor Updates:

1. dxCompiler compatible.
2. Updated HTML Statistics definitions links, all links are directed to /docs/definitions.md.
3. Effective Genome Size & Effective Genome Fraction are auto-calculated from Genome FASTA.
4. SEAseq, ROSE, BAM2GFF docker image updates to reflect relevant changes.

SEAseq version 2.1

SEAseq version 2.1
Minor Update:

• Host Genomes or Custom Genome selection.
  Genomes provided are hg19, hg38, mm9 and mm10. More information on genome files used can be found in /docs.

SEAseq version 2

SEAseq version 2
Major Update:

• Enabled for ChIP-seq control or IgG.
• Two script versions for SEAseq:
  - seaseq-case.wdl for ChIP/CutNRun Samples only
  - seaseq-control.wdl for ChIP/CutNRun Samples and Input/Control.

Others:

• Changed name variables for FASTQ files as : control_fastq for Input/Control FASTQ file(s), control_sraid for Input/Control SRA identifier(s) (SRR(s)), sample.fastq for sample FASTQ file(s), sample_sraid for sample SRR(s)

SEAseq v1.1

upgrades from version 1.0

• Motif "Prediction" Analysis is now optional.
• Peak Annotation Analysis on all versions of peaks
• Accepts zipped genome (.fa), blacklist (.bed) and gene annotation (.gtf/.gff) files
• Accepts annotation from gff and gff3 from all genomes
• Removed genome hard-coding on SICER, ROSE and BAMTOGFF.
• Merge the multiple fastqs and preliminary (fastqc + mapping) analysis for the individual fastqs

SEAseq

Single End Antibody sequencing pipeline