| Parameter | Value |
|---|---|
| Project Name | pluripotency_exit_EpiLC_DNMT_ATAC.smk |
| Vistory Name | pluripotency_exit_EpiLC_DNMT_ATAC_pmQC.smv |
| Genome | Mus musculus GRCm38_v95 |
| SeqMonk Version | 1.45.3.devel |
| Name | File Name | Reads | Import Options |
|---|---|---|---|
| lane7005_AAGAGGCA_Dnmt13_KO_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_AAGAGGCA_Dnmt13_KO_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 6603687 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_ACCACTGT_Dnmt13_KO_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_ACCACTGT_Dnmt13_KO_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 4078703 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_AGGCAGAA_Dnmt13_WT_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_AGGCAGAA_Dnmt13_WT_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 8295584 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_CAGAGAGG_Dnmt13_WT_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_CAGAGAGG_Dnmt13_WT_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 6263183 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_CCGTTTGT_Dnmt13_KO_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_CCGTTTGT_Dnmt13_KO_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 7554053 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_CGAGGCTG_Dnmt13_KO_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_CGAGGCTG_Dnmt13_KO_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 6462225 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_CGTACTAG_Dnmt13_WT_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_CGTACTAG_Dnmt13_WT_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 6435280 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_CTCTCTAC_Dnmt13_WT_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_CTCTCTAC_Dnmt13_WT_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 7195699 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_GAGGGGTT_Dnmt13_KO_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_GAGGGGTT_Dnmt13_KO_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 6457724 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_GCTACGCT_Dnmt13_WT_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_GCTACGCT_Dnmt13_WT_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 5706778 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_GGACTCCT_Dnmt13_WT_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_GGACTCCT_Dnmt13_WT_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 9489631 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_GTAGAGGA_Dnmt13_KO_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_GTAGAGGA_Dnmt13_KO_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 6343782 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_GTCGTGAT_Dnmt13_KO_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_GTCGTGAT_Dnmt13_KO_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 6459710 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_TAAGGCGA_Dnmt13_WT_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_TAAGGCGA_Dnmt13_WT_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 7904469 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_TAGGCATG_Dnmt13_WT_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_TAGGCATG_Dnmt13_WT_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 4072943 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_TCCTGAGC_Dnmt13_WT_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_TCCTGAGC_Dnmt13_WT_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 7773108 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_TGCTGGGT_Dnmt13_KO_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_TGCTGGGT_Dnmt13_KO_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 6011131 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| lane7005_TGGATCTG_Dnmt13_KO_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam | /bi/seqfac/seqfac/191007_D00436_0478_BHY7NMBCX2/Aligned/Project_HY7NMBCX2/Sample_lane1/lane7005_TGGATCTG_Dnmt13_KO_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 5873800 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
Data Set Renamed
lane7005_AAGAGGCA_Dnmt13_KO_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_AAGAGGCA_Dnmt13_KO_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_ACCACTGT_Dnmt13_KO_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_ACCACTGT_Dnmt13_KO_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_AGGCAGAA_Dnmt13_WT_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_AGGCAGAA_Dnmt13_WT_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CAGAGAGG_Dnmt13_WT_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_CAGAGAGG_Dnmt13_WT_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CCGTTTGT_Dnmt13_KO_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_CCGTTTGT_Dnmt13_KO_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CGAGGCTG_Dnmt13_KO_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_CGAGGCTG_Dnmt13_KO_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CGTACTAG_Dnmt13_WT_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_CGTACTAG_Dnmt13_WT_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CTCTCTAC_Dnmt13_WT_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_CTCTCTAC_Dnmt13_WT_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GAGGGGTT_Dnmt13_KO_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_GAGGGGTT_Dnmt13_KO_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GCTACGCT_Dnmt13_WT_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_GCTACGCT_Dnmt13_WT_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GGACTCCT_Dnmt13_WT_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_GGACTCCT_Dnmt13_WT_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GTAGAGGA_Dnmt13_KO_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_GTAGAGGA_Dnmt13_KO_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GTCGTGAT_Dnmt13_KO_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_GTCGTGAT_Dnmt13_KO_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TAAGGCGA_Dnmt13_WT_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_TAAGGCGA_Dnmt13_WT_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TAGGCATG_Dnmt13_WT_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_TAGGCATG_Dnmt13_WT_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TCCTGAGC_Dnmt13_WT_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_TCCTGAGC_Dnmt13_WT_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TGCTGGGT_Dnmt13_KO_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_TGCTGGGT_Dnmt13_KO_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TGGATCTG_Dnmt13_KO_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to lane7005_TGGATCTG_Dnmt13_KO_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_AAGAGGCA_Dnmt13_KO_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_ACCACTGT_Dnmt13_KO_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_AGGCAGAA_Dnmt13_WT_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CAGAGAGG_Dnmt13_WT_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CCGTTTGT_Dnmt13_KO_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CGAGGCTG_Dnmt13_KO_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CGTACTAG_Dnmt13_WT_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_CTCTCTAC_Dnmt13_WT_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GAGGGGTT_Dnmt13_KO_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GCTACGCT_Dnmt13_WT_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GGACTCCT_Dnmt13_WT_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GTAGAGGA_Dnmt13_KO_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_GTCGTGAT_Dnmt13_KO_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TAAGGCGA_Dnmt13_WT_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TAGGCATG_Dnmt13_WT_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TCCTGAGC_Dnmt13_WT_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TGCTGGGT_Dnmt13_KO_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
lane7005_TGGATCTG_Dnmt13_KO_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam
Data Set Renamed
ATAC_Dnmt13_KO_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_0_2
Data Set Renamed
ATAC_Dnmt13_KO_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_1_2
Data Set Renamed
ATAC_Dnmt13_WT_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_0_3
Data Set Renamed
ATAC_Dnmt13_WT_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_2_2
Data Set Renamed
ATAC_Dnmt13_KO_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_2_1
Data Set Renamed
ATAC_Dnmt13_KO_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_0_1
Data Set Renamed
ATAC_Dnmt13_WT_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_0_2
Data Set Renamed
ATAC_Dnmt13_WT_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_2_1
Data Set Renamed
ATAC_Dnmt13_KO_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_2_3
Data Set Renamed
ATAC_Dnmt13_WT_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_2_3
Data Set Renamed
ATAC_Dnmt13_WT_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_1_2
Data Set Renamed
ATAC_Dnmt13_KO_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_0_3
Data Set Renamed
ATAC_Dnmt13_KO_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_1_1
Data Set Renamed
ATAC_Dnmt13_WT_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_0_1
Data Set Renamed
ATAC_Dnmt13_WT_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_1_3
Data Set Renamed
ATAC_Dnmt13_WT_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_WT_Day_1_1
Data Set Renamed
ATAC_Dnmt13_KO_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_2_2
Data Set Renamed
ATAC_Dnmt13_KO_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam changed to ATAC_Dnmt13_KO_Day_1_3
Replicate Set Created
ATAC_Dnmt13_KO_Day_0 ATAC_Dnmt13_KO_Day_0_1 ATAC_Dnmt13_KO_Day_0_2 ATAC_Dnmt13_KO_Day_0_3
Replicate Set Created
ATAC_Dnmt13_KO_Day_1 ATAC_Dnmt13_KO_Day_1_1 ATAC_Dnmt13_KO_Day_1_2 ATAC_Dnmt13_KO_Day_1_3
Replicate Set Created
ATAC_Dnmt13_KO_Day_2 ATAC_Dnmt13_KO_Day_2_1 ATAC_Dnmt13_KO_Day_2_2 ATAC_Dnmt13_KO_Day_2_3
Replicate Set Created
ATAC_Dnmt13_WT_Day_0 ATAC_Dnmt13_WT_Day_0_1 ATAC_Dnmt13_WT_Day_0_2 ATAC_Dnmt13_WT_Day_0_3
Replicate Set Created
ATAC_Dnmt13_WT_Day_1 ATAC_Dnmt13_WT_Day_1_1 ATAC_Dnmt13_WT_Day_1_2 ATAC_Dnmt13_WT_Day_1_3
Replicate Set Created
ATAC_Dnmt13_WT_Day_2 ATAC_Dnmt13_WT_Day_2_1 ATAC_Dnmt13_WT_Day_2_2 ATAC_Dnmt13_WT_Day_2_3
New Probe Set (2725549 probes)
Running windows of size 1000 with step size 1000
Probes Quantitated
Read Count Quantitation using All Reads correcting for total count per million reads log transformed
| DataStore | Total Read Count | Forward Read Count | Reverse Read Count | Unknown Read Count | Mean Read Length | Total Read Length | Fold Coverage | Total Quantitation | Median Quantitation | Mean Quantitation | Valid Quantitations |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ATAC_Dnmt13_WT_Day_0_1 | 7904469 | 3949269 | 3955200 | 0 | 298 | 2358739165 | 0.8654215980311223 | -5038518.777562784 | -1.9826686 | -1.8486253 | 2725549 |
| ATAC_Dnmt13_WT_Day_0_2 | 6435280 | 3214165 | 3221115 | 0 | 298 | 1919229657 | 0.7041655225789506 | -4692138.88761875 | -1.686003 | -1.721539 | 2725549 |
| ATAC_Dnmt13_WT_Day_0_3 | 8295584 | 4147000 | 4148584 | 0 | 298 | 2472721063 | 0.9072415659942948 | -4605709.728179067 | -1.4673811 | -1.6898283 | 2725549 |
| ATAC_Dnmt13_WT_Day_1_1 | 7773108 | 3877836 | 3895272 | 0 | 298 | 2321274131 | 0.851675673905353 | -5145094.312837571 | -1.9584917 | -1.8877277 | 2725549 |
| ATAC_Dnmt13_WT_Day_1_2 | 9489631 | 4737461 | 4752170 | 0 | 298 | 2834220614 | 1.0398757816617796 | -5340681.762780331 | -1.6613896 | -1.9594884 | 2725549 |
| ATAC_Dnmt13_WT_Day_1_3 | 4072943 | 2034985 | 2037958 | 0 | 298 | 1216803923 | 0.4464454616935988 | -3761603.1464116685 | -2.0260718 | -1.3801267 | 2725549 |
| ATAC_Dnmt13_WT_Day_2_1 | 7195699 | 3592987 | 3602712 | 0 | 298 | 2148083763 | 0.7881321133191793 | -4937615.169568609 | -1.8471348 | -1.8116039 | 2725549 |
| ATAC_Dnmt13_WT_Day_2_2 | 6263183 | 3128325 | 3134858 | 0 | 298 | 1869077009 | 0.6857645118094312 | -4704241.659865901 | -1.646896 | -1.7259794 | 2725549 |
| ATAC_Dnmt13_WT_Day_2_3 | 5706778 | 2849537 | 2857241 | 0 | 298 | 1704993693 | 0.6255623293680481 | -4242784.615774855 | -1.5126765 | -1.5566716 | 2725549 |
| ATAC_Dnmt13_KO_Day_0_1 | 6462225 | 3232859 | 3229366 | 0 | 298 | 1930492629 | 0.7082979079530748 | -4192553.3062986955 | -1.692031 | -1.5382417 | 2725549 |
| ATAC_Dnmt13_KO_Day_0_2 | 6603687 | 3304799 | 3298888 | 0 | 298 | 1970795283 | 0.7230849550955152 | -4885110.026117712 | -1.7232716 | -1.7923398 | 2725549 |
| ATAC_Dnmt13_KO_Day_0_3 | 6343782 | 3172498 | 3171284 | 0 | 298 | 1895170469 | 0.6953382044781418 | -4760287.063620113 | -1.665343 | -1.7465425 | 2725549 |
| ATAC_Dnmt13_KO_Day_1_1 | 6459710 | 3228865 | 3230845 | 0 | 298 | 1928558610 | 0.7075883162193052 | -4565574.1212581545 | -1.6914694 | -1.6751026 | 2725549 |
| ATAC_Dnmt13_KO_Day_1_2 | 4078703 | 2035874 | 2042829 | 0 | 298 | 1217627803 | 0.446747743334895 | -3708263.963364454 | -2.0281105 | -1.3605567 | 2725549 |
| ATAC_Dnmt13_KO_Day_1_3 | 5873800 | 2929460 | 2944340 | 0 | 299 | 1757587742 | 0.6448590903698128 | -5575165.583618002 | -2.554294 | -2.0455203 | 2725549 |
| ATAC_Dnmt13_KO_Day_2_1 | 7554053 | 3775877 | 3778176 | 0 | 298 | 2253796121 | 0.8269179863608042 | -4240913.53544195 | -1.3322885 | -1.5559851 | 2725549 |
| ATAC_Dnmt13_KO_Day_2_2 | 6011131 | 3005657 | 3005474 | 0 | 298 | 1796163722 | 0.6590126206764233 | -4105289.3457592567 | -1.5876365 | -1.5062248 | 2725549 |
| ATAC_Dnmt13_KO_Day_2_3 | 6457724 | 3228249 | 3229475 | 0 | 299 | 1930919380 | 0.7084544829308687 | -4407235.808466345 | -1.6910257 | -1.6170084 | 2725549 |
Slightly unbalanced read counts, watch when peak calling.
Could be prettier ....
New Probe List: Value above 0 (226605 probes)
[Probe Values Filter] Filter on probes in 1kb tiles where at least 1 of ATAC_Dnmt13_KO_Day_0 , ATAC_Dnmt13_KO_Day_1 , ATAC_Dnmt13_KO_Day_2 , ATAC_Dnmt13_WT_Day_0 , ATAC_Dnmt13_WT_Day_1 , ATAC_Dnmt13_WT_Day_2 had a value above 0.0. Quantitation was Read Count Quantitation using All Reads correcting for total count per million reads log transformed
Probe List Renamed
Probe list Value above 0 renamed to Value above 0 in any
There is some variation in duplication between replicates, but it's not really enough to explain the difference in PC1 or in the tree.
A bit hard to say, but there may overall not be that much difference between the sample groups.
New Probe List: Value below 4 in all (2725452 probes)
[Probe Values Filter] Filter on probes in 1kb tiles where exactly 6 of ATAC_Dnmt13_KO_Day_0 , ATAC_Dnmt13_KO_Day_1 , ATAC_Dnmt13_KO_Day_2 , ATAC_Dnmt13_WT_Day_0 , ATAC_Dnmt13_WT_Day_1 , ATAC_Dnmt13_WT_Day_2 had a value below 4.0. Quantitation was Read Count Quantitation using All Reads correcting for total count per million reads log transformed
