======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

{{:fastqc_bs-tag_gtagagg_r1.pdf|}} 

{{:fastqc_bs-tag_gtagagg_r2.pdf|}}

Results of fastqc on adapter trimmed (with skewer) and PCR duplicate removed (with Fastuniq) 

{{::fastqc_bs_tag_noadap_pair1.pdf|}}

{{::fastqc_bs_tag_noadap_pair2.pdf|}}


===== Preqc (SGA preprocessing) results =====

Sun May 24

{{:ucsf_bs-tag_preqc_report.pdf|}}

Preqc report was also run for the UCSF BS-MK and BS-tag data (pooled).

{{:ucsf_new_lib_preqc_report.pdf|}}

==== 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

{{::fastqc_bs-tag_seqprep_dupremoved_r1.pdf|}}

{{::fastqc_bs-tag_seqprep_dupremoved_r2.pdf|}}