| Parameter | Value |
|---|---|
| Project Name | pluripotency_exit_EpiLC.smk |
| Vistory Name | pluripotency_exit_EpiLC_ATACSeq_QC.smv |
| Genome | Mus musculus GRCm38_v95 |
| SeqMonk Version | 1.45.4 |
| Name | File Name | Reads | Import Options |
|---|---|---|---|
| ATAC_TET_KO_Day_0_1 | C:\Users\kruegerc\Downloads\lane6640_CGAGGCTG_TET_KO_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 9231171 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_KO_Day_0_2 | C:\Users\kruegerc\Downloads\lane6640_AAGAGGCA_TET_KO_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 7490158 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_KO_Day_0_3 | C:\Users\kruegerc\Downloads\lane6640_GTAGAGGA_TET_KO_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 7538296 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_KO_Day_1_1 | C:\Users\kruegerc\Downloads\lane6640_GTCGTGAT_TET_KO_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 8691512 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_KO_Day_1_2 | C:\Users\kruegerc\Downloads\lane6640_ACCACTGT_TET_KO_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 9626783 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_KO_Day_1_3 | C:\Users\kruegerc\Downloads\lane6640_TGGATCTG_TET_KO_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 7067327 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_KO_Day_2_1 | C:\Users\kruegerc\Downloads\lane6640_CCGTTTGT_TET_KO_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 7544384 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_KO_Day_2_3 | C:\Users\kruegerc\Downloads\lane6640_GAGGGGTT_TET_KO_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 13002851 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_WT_Day_0_1 | C:\Users\kruegerc\Downloads\lane6640_TAAGGCGA_TET_WT_Day_0_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 21585546 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_WT_Day_0_2 | C:\Users\kruegerc\Downloads\lane6640_CGTACTAG_TET_WT_Day_0_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 9370148 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_WT_Day_0_3 | C:\Users\kruegerc\Downloads\lane6640_AGGCAGAA_TET_WT_Day_0_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 12334582 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_WT_Day_1_1 | C:\Users\kruegerc\Downloads\lane6640_TCCTGAGC_TET_WT_Day_1_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 9762146 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_WT_Day_1_2 | C:\Users\kruegerc\Downloads\lane6640_GGACTCCT_TET_WT_Day_1_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 7906770 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_WT_Day_1_3 | C:\Users\kruegerc\Downloads\lane6640_TAGGCATG_TET_WT_Day_1_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 8713090 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_WT_Day_2_1 | C:\Users\kruegerc\Downloads\lane6640_CTCTCTAC_TET_WT_Day_2_1_L001_R1_trimmed_GRCm38_bowtie2.bam | 9949866 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_WT_Day_2_2 | C:\Users\kruegerc\Downloads\lane6640_CAGAGAGG_TET_WT_Day_2_2_L001_R1_trimmed_GRCm38_bowtie2.bam | 9090098 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| ATAC_TET_WT_Day_2_3 | C:\Users\kruegerc\Downloads\lane6640_GCTACGCT_TET_WT_Day_2_3_L001_R1_trimmed_GRCm38_bowtie2.bam | 11878476 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 250 |
| RNA_EpiLC_TET_KO_1.2 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_KO_1.2_TGCATAGT_L002_3536STDY7824960_R1_val_1_GRCm38_hisat2.bam | 16874035 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_KO_1.3 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_KO_1.3_TTGACTCT_L002_3536STDY7824961_R1_val_1_GRCm38_hisat2.bam | 17434295 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_KO_2.1 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_KO_2.1_TGCGATCT_L002_3536STDY7824962_R1_val_1_GRCm38_hisat2.bam | 11207558 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_KO_2.2 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_KO_2.2_TTCCTGCT_L002_3536STDY7824963_R1_val_1_GRCm38_hisat2.bam | 14823541 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_KO_2.3 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_KO_2.3_TAGTGACT_L002_3536STDY7824964_R1_val_1_GRCm38_hisat2.bam | 11753184 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_WT_1.1 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_WT_1.1_TGACCACT_L002_3536STDY7824941_R1_val_1_GRCm38_hisat2.bam | 15243831 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_WT_1.2 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_WT_1.2_ACAGTGGT_L002_3536STDY7824942_R1_val_1_GRCm38_hisat2.bam | 15746324 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_WT_1.3 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_WT_1.3_GCCAATGT_L002_3536STDY7824943_R1_val_1_GRCm38_hisat2.bam | 15153879 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_WT_2.1 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_WT_2.1_CAGATCTG_L002_3536STDY7824944_R1_val_1_GRCm38_hisat2.bam | 16306230 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_WT_2.2 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_WT_2.2_ACTTGATG_L002_3536STDY7824945_R1_val_1_GRCm38_hisat2.bam | 15384704 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_EpiLC_TET_WT_2.3 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_EpiLC_TET_WT_2.3_GATCAGCG_L002_3536STDY7824946_R1_val_1_GRCm38_hisat2.bam | 15677071 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_mESC_TET_KO_2iL_0.1 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_mESC_TET_KO_2iL_0.1_TCTGCTGT_L002_3536STDY7824956_R1_val_1_GRCm38_hisat2.bam | 15387124 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_mESC_TET_KO_2iL_0.2 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_mESC_TET_KO_2iL_0.2_TTGGAGGT_L002_3536STDY7824957_R1_val_1_GRCm38_hisat2.bam | 16272122 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_mESC_TET_KO_2iL_0.3 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_mESC_TET_KO_2iL_0.3_TCGAGCGT_L002_3536STDY7824958_R1_val_1_GRCm38_hisat2.bam | 15148806 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_mESC_TET_WT_2iL_0.1 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_mESC_TET_WT_2iL_0.1_ATCACGTT_L002_3536STDY7824938_R1_val_1_GRCm38_hisat2.bam | 15744729 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_mESC_TET_WT_2iL_0.2 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_mESC_TET_WT_2iL_0.2_CGATGTTT_L002_3536STDY7824939_R1_val_1_GRCm38_hisat2.bam | 14030096 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| RNA_mESC_TET_WT_2iL_0.3 | /bi/seqfac/seqfac/190324_Tim_Globus/Aligned/Project_Sanger/Sample_lane2/lane2_mESC_TET_WT_2iL_0.3_TTAGGCAT_L002_3536STDY7824940_R1_val_1_GRCm38_hisat2.bam | 17068154 | Library type Paired End Dedup=No MAPQ>=20 Primary alignments only. Treat as RNA-Seq dataPaired distance cutoff = 1000 |
| ATAC_TET_KO_Day_0 | ATAC_TET_KO_Day_1 | ATAC_TET_KO_Day_2 | ATAC_TET_WT_Day_0 | ATAC_TET_WT_Day_1 | ATAC_TET_WT_Day_2 | RNA_EpiLC_TET_KO_1 | RNA_EpiLC_TET_KO_2 | RNA_EpiLC_TET_WT_1 | RNA_EpiLC_TET_WT_2 | RNA_mESC_TET_KO | RNA_mESC_TET_WT |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ATAC_TET_KO_Day_0_1 | ATAC_TET_KO_Day_1_1 | ATAC_TET_KO_Day_2_1 | ATAC_TET_WT_Day_0_1 | ATAC_TET_WT_Day_1_1 | ATAC_TET_WT_Day_2_1 | RNA_EpiLC_TET_KO_1.2 | RNA_EpiLC_TET_KO_2.1 | RNA_EpiLC_TET_WT_1.1 | RNA_EpiLC_TET_WT_2.1 | RNA_mESC_TET_KO_2iL_0.1 | RNA_mESC_TET_WT_2iL_0.1 |
| ATAC_TET_KO_Day_0_2 | ATAC_TET_KO_Day_1_2 | ATAC_TET_KO_Day_2_3 | ATAC_TET_WT_Day_0_2 | ATAC_TET_WT_Day_1_2 | ATAC_TET_WT_Day_2_2 | RNA_EpiLC_TET_KO_1.3 | RNA_EpiLC_TET_KO_2.2 | RNA_EpiLC_TET_WT_1.2 | RNA_EpiLC_TET_WT_2.2 | RNA_mESC_TET_KO_2iL_0.2 | RNA_mESC_TET_WT_2iL_0.2 |
| ATAC_TET_KO_Day_0_3 | ATAC_TET_KO_Day_1_3 | ATAC_TET_WT_Day_0_3 | ATAC_TET_WT_Day_1_3 | ATAC_TET_WT_Day_2_3 | RNA_EpiLC_TET_KO_2.3 | RNA_EpiLC_TET_WT_1.3 | RNA_EpiLC_TET_WT_2.3 | RNA_mESC_TET_KO_2iL_0.3 | RNA_mESC_TET_WT_2iL_0.3 |
| Name | Parent | Probes | Description | Comments |
|---|---|---|---|---|
| 1kb tiles | 2725549 | Running windows of size 1000 with step size 1000. Quantitated with 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_TET_KO_Day_0_1 | 9231171 | 4617139 | 4614032 | 0 | 299 | 2762491166 | 1.013558241157444 | -4418136.808083598 | -1.6215512 | -1.621008 | 2725549 |
| ATAC_TET_KO_Day_0_2 | 7490158 | 3745442 | 3744716 | 0 | 299 | 2239785068 | 0.82177732983664 | -4730509.963961691 | -1.904996 | -1.7356173 | 2725549 |
| ATAC_TET_KO_Day_0_3 | 7538296 | 3772548 | 3765748 | 0 | 299 | 2257557238 | 0.8282979405044503 | -5220905.878709063 | -1.9142385 | -1.9155428 | 2725549 |
| ATAC_TET_KO_Day_1_1 | 8691512 | 4346473 | 4345039 | 0 | 299 | 2599768271 | 0.9538551972953855 | -4419204.114937741 | -1.5346447 | -1.6213996 | 2725549 |
| ATAC_TET_KO_Day_1_2 | 9626783 | 4808311 | 4818472 | 0 | 299 | 2880650668 | 1.0569109723795933 | -5429912.522492781 | -1.6820912 | -1.9922271 | 2725549 |
| ATAC_TET_KO_Day_1_3 | 7067327 | 3540764 | 3526563 | 0 | 299 | 2115090262 | 0.776026795027209 | -5395841.384016116 | -1.8211647 | -1.9797264 | 2725549 |
| ATAC_TET_KO_Day_2_1 | 7544384 | 3775048 | 3769336 | 0 | 299 | 2257134369 | 0.8281427898327829 | -4900216.601823255 | -1.9154031 | -1.7978824 | 2725549 |
| ATAC_TET_KO_Day_2_3 | 13002851 | 6506135 | 6496716 | 0 | 299 | 3890314902 | 1.4273568647566544 | -4817487.678001393 | -1.378828 | -1.7675292 | 2725549 |
| ATAC_TET_WT_Day_0_1 | 21585546 | 10791143 | 10794403 | 0 | 299 | 6459324984 | 2.3699268799208806 | -4536503.38598299 | -1.4319937 | -1.6644366 | 2725549 |
| ATAC_TET_WT_Day_0_2 | 9370148 | 4684524 | 4685624 | 0 | 299 | 2805017696 | 1.0291612285913339 | -4289848.231064033 | -1.2280718 | -1.5739391 | 2725549 |
| ATAC_TET_WT_Day_0_3 | 12334582 | 6172680 | 6161902 | 0 | 299 | 3692570354 | 1.3548043734632382 | -4908705.568695381 | -1.6246369 | -1.800997 | 2725549 |
| ATAC_TET_WT_Day_1_1 | 9762146 | 4880768 | 4881378 | 0 | 299 | 2921822142 | 1.0720167896531096 | -4497956.025721792 | -1.7022358 | -1.6502936 | 2725549 |
| ATAC_TET_WT_Day_1_2 | 7906770 | 3951816 | 3954954 | 0 | 299 | 2368237348 | 0.8689064821727107 | -4923099.6371498015 | -1.9830886 | -1.8062781 | 2725549 |
| ATAC_TET_WT_Day_1_3 | 8713090 | 4356768 | 4356322 | 0 | 299 | 2606694725 | 0.9563965138505668 | -4702463.9383103475 | -1.538222 | -1.7253273 | 2725549 |
| ATAC_TET_WT_Day_2_1 | 9949866 | 4973079 | 4976787 | 0 | 299 | 2977303990 | 1.092373084350866 | -4264210.800279714 | -1.3146771 | -1.5645328 | 2725549 |
| ATAC_TET_WT_Day_2_2 | 9090098 | 4545610 | 4544488 | 0 | 299 | 2719217773 | 0.997681229626036 | -5047485.227517334 | -1.5993334 | -1.851915 | 2725549 |
| ATAC_TET_WT_Day_2_3 | 11878476 | 5934848 | 5943628 | 0 | 299 | 3554886237 | 1.3042880593553814 | -4795332.011099329 | -1.5702778 | -1.7594004 | 2725549 |
Somewhat unbalanced read counts, may want to do something about it if peak calling.
Probes Quantitated
Read Count Quantitation using All Reads correcting for total count per million reads
Read locations make sense.
Probes Quantitated
Read Count Quantitation using All Reads correcting for total count per million reads log transformed
New Probe List: Value above 0 in any (214162 probes)
[Probe Values Filter] Filter on probes in 1kb tiles where at least 1 of ATAC_TET_KO_Day_0 , ATAC_TET_KO_Day_1 , ATAC_TET_KO_Day_2 , ATAC_TET_WT_Day_0 , ATAC_TET_WT_Day_1 , ATAC_TET_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
Filtering on at least one probe > 0 makes more sense; PC1 genotype and PC2 timepoint
