Updates to MethylSeq pipeline GL-DPPD-7113 #130
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bnovak32
commented
Nov 7, 2024
bnovak32
commented
- Updates sorting of BAM files to fix Issue [Methyl-Seq] Pipeline specifies incorrect input for deduplication step. #94
- Update external documentation links
- Update software versions
- Add additional report summaries
- Add clipping parameter specifications for random priming library preps
- Added an alignment multiqc step that gathers all qualimap and bismark alignment QC reports (Step 9b) - Added trimgalore reports to trimmed multiqc report - Added report suffixes (GLMethylSeq) to all multiqc reports - Updated multicore specification from "4" to "NumberOfThreads" - Updated filename specifications to more specifically call out the different filenames bismark generates for paired-end/single-end, bowtie2/hisat2 - Moved generation of nucleotide frequencies file from alignment step to genome reference generation step - Updated R library versions
Updates tool versions, and fixes issues with PE datasets
- added clipping parameters for random-priming library type - added gzip parameter to bismark alignment command to reduce intermediate file size
Clipping and performance updates added clipping parameters for random-priming library type added gzip parameter to bismark alignment command to reduce intermediate file size
Updated TOC with link to newly added trimming option.
Updated TOC with link to newly added trimming option.
Added missing UCSC tools to software table.
Updating tool versions and adding missing tools
update FastQC version
update FastQC version
Specified genomic_nucleotide_frequencies.txt as an output file.
Fix typos
Updated broken documentation link
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