Table of Contents
BS-tag
Sequencing data
| Library | Run | Location | Notes |
| /campusdata/BME235/Spring2015Data/UCSF_BS-tag/ |
Adapter sequences:
Tn5ME-A (Illumina FC-121-1030): 5'-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3'
Tn5ME-B (Illumina FC-121-1031): 5'-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG- 3'
Files
| File | Size |
| BS-tag_GTAGAGG_R1.fastq | 36G |
| BS-tag_GTAGAGG_R2.fastq | 36G |
| ../preqc/ucsf_bs-tag/ucsf_bs-tag.fastq | 74G |
| ../adapter_trimming/UCSF_reads_skewer_trimmed/BS_tag_noAdap_pair1.fastq | 36G |
| ../adapter_trimming/UCSF_reads_skewer_trimmed/BS_tag_noAdap_pair2.fastq | 36G |
| ../merging/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_merged.fastq.gz | 7.5G |
| ../merging/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R1_trimmed.fastq.gz | 3.0G |
| ../merging/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R2_trimmed.fastq.gz | 3.0G |
| /campusdata/BME235/Spring2015Data/ErrorCorrected/BS-tag_seqprep_dupRemoved_ec_R1.fastq | 9.0G |
| /campusdata/BME235/Spring2015Data/ErrorCorrected/BS-tag_seqprep_dupRemoved_ec_R2.fastq | 9.0G |
FastQC results
Results of the run are located here on the campusrocks2 server:
/campusdata/BME235/S15_assemblies/SOAPdenovo2/Fastqc/UCSF_BS-tag_fastqc
Results of fastqc on adapter trimmed (with skewer) and PCR duplicate removed (with Fastuniq)
Preqc (SGA preprocessing) results
Sun May 24
Preqc report was also run for the UCSF BS-MK and BS-tag data (pooled).
Comments
The preqc report for the ucsf_bs-tag reads look similar to previous reports. The ucsf_bs-tag is not represented in the k-de Bruijn graphs indicating insufficient coverage to make these predictions. This report provides a useful baseline for comparison with other pre-processing efforts.
SeqPrep results
The data files were trimmed using SeqPrep, both with and without merging. The output for the run without merging is in /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData and the output for the run with merging is in /campusdata/BME235/Spring2015Data/merging/SeqPrep_newData. The trimmed R1 and R2 files for the run with merging are much smaller than those from the non-merging run.
The adapters used for both runs were CTGTCTCTTATACACATCTCCGAGCCCACGAGAC (-A option) and CTGTCTCTTATACACATCTGACGCTGCCGACGA (-B option).
FastQC on Seqprep, Fastuniq, Musket processed files
Seqprep adapter removed files were run through Fastuniq to remove PCR duplicates, then through musket for error correction, and lastly FastQC for analysis
