| Parameter | Value |
|---|---|
| Project Name | pluripotency_exit_hmC.smk |
| Vistory Name | pluripotency_exit_hmC_210513.smv |
| Genome | Mus musculus GRCm38_v100 |
| SeqMonk Version | 1.48.0 |
| Name | File Name | Reads | Import Options |
|---|---|---|---|
| lane7624_AAGTCCA_TET_WT_1_1_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_AAGTCCA_TET_WT_1_1_L001_GRCm38_bowtie2.bam | 5066125 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_AATGCCT_DNMT_WT_2_2_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_AATGCCT_DNMT_WT_2_2_L001_GRCm38_bowtie2.bam | 14178685 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_AGTTCAG_TET_WT_2_3_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_AGTTCAG_TET_WT_2_3_L001_GRCm38_bowtie2.bam | 23573019 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_ATCCACT_TET_WT_1_2_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_ATCCACT_TET_WT_1_2_L001_GRCm38_bowtie2.bam | 6321146 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_CAAGCTA_TET_WT_2_1_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_CAAGCTA_TET_WT_2_1_L001_GRCm38_bowtie2.bam | 24178991 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_CCGCGGT_TET_WT_0_1_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_CCGCGGT_TET_WT_0_1_L001_GRCm38_bowtie2.bam | 44463991 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_GCTTGTC_TET_WT_1_3_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_GCTTGTC_TET_WT_1_3_L001_GRCm38_bowtie2.bam | 23661978 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_GGACTTG_TET_WT_0_3_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_GGACTTG_TET_WT_0_3_L001_GRCm38_bowtie2.bam | 42584273 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_GGCATTC_DNMT_WT_2_1_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_GGCATTC_DNMT_WT_2_1_L001_GRCm38_bowtie2.bam | 35637001 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_TACCGAG_DNMT_WT_2_3_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_TACCGAG_DNMT_WT_2_3_L001_GRCm38_bowtie2.bam | 25518826 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_TGGATCG_TET_WT_2_2_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_TGGATCG_TET_WT_2_2_L001_GRCm38_bowtie2.bam | 17411480 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
| lane7624_TTATAAC_TET_WT_0_2_L001_GRCm38_bowtie2.bam | C:\Users\kruegerc\Downloads\lane7624_TTATAAC_TET_WT_0_2_L001_GRCm38_bowtie2.bam | 25705722 | Library type Single End Dedup=No MAPQ>=20 Primary alignments only. Extend reads by 225 |
Data Set Renamed
lane7624_AAGTCCA_TET_WT_1_1 changed to lane7624_AAGTCCA_TET_WT_1_1
Data Set Renamed
lane7624_AATGCCT_DNMT_WT_2_2_L001_GRCm38_bowtie2.bam changed to lane7624_AATGCCT_DNMT_WT_2_2
Data Set Renamed
lane7624_AGTTCAG_TET_WT_2_3_L001_GRCm38_bowtie2.bam changed to lane7624_AGTTCAG_TET_WT_2_3
Data Set Renamed
lane7624_ATCCACT_TET_WT_1_2_L001_GRCm38_bowtie2.bam changed to lane7624_ATCCACT_TET_WT_1_2
Data Set Renamed
lane7624_CAAGCTA_TET_WT_2_1_L001_GRCm38_bowtie2.bam changed to lane7624_CAAGCTA_TET_WT_2_1
Data Set Renamed
lane7624_CCGCGGT_TET_WT_0_1_L001_GRCm38_bowtie2.bam changed to lane7624_CCGCGGT_TET_WT_0_1
Data Set Renamed
lane7624_GCTTGTC_TET_WT_1_3_L001_GRCm38_bowtie2.bam changed to lane7624_GCTTGTC_TET_WT_1_3
Data Set Renamed
lane7624_GGACTTG_TET_WT_0_3_L001_GRCm38_bowtie2.bam changed to lane7624_GGACTTG_TET_WT_0_3
Data Set Renamed
lane7624_GGCATTC_DNMT_WT_2_1_L001_GRCm38_bowtie2.bam changed to lane7624_GGCATTC_DNMT_WT_2_1
Data Set Renamed
lane7624_TACCGAG_DNMT_WT_2_3_L001_GRCm38_bowtie2.bam changed to lane7624_TACCGAG_DNMT_WT_2_3
Data Set Renamed
lane7624_TGGATCG_TET_WT_2_2_L001_GRCm38_bowtie2.bam changed to lane7624_TGGATCG_TET_WT_2_2
Data Set Renamed
lane7624_TTATAAC_TET_WT_0_2_L001_GRCm38_bowtie2.bam changed to lane7624_TTATAAC_TET_WT_0_2
Data Set Renamed
lane7624_AAGTCCA_TET_WT_1_1 changed to TET_WT_1_1
Data Set Renamed
lane7624_AATGCCT_DNMT_WT_2_2 changed to DNMT_WT_2_2
Data Set Renamed
lane7624_AGTTCAG_TET_WT_2_3 changed to TET_WT_2_3
Data Set Renamed
lane7624_ATCCACT_TET_WT_1_2 changed to TET_WT_1_2
Data Set Renamed
lane7624_CAAGCTA_TET_WT_2_1 changed to TET_WT_2_1
Data Set Renamed
lane7624_CCGCGGT_TET_WT_0_1 changed to TET_WT_0_1
Data Set Renamed
lane7624_GCTTGTC_TET_WT_1_3 changed to TET_WT_1_3
Data Set Renamed
lane7624_GGACTTG_TET_WT_0_3 changed to TET_WT_0_3
Data Set Renamed
lane7624_GGCATTC_DNMT_WT_2_1 changed to DNMT_WT_2_1
Data Set Renamed
lane7624_TACCGAG_DNMT_WT_2_3 changed to DNMT_WT_2_3
Data Set Renamed
lane7624_TGGATCG_TET_WT_2_2 changed to TET_WT_2_2
Data Set Renamed
lane7624_TTATAAC_TET_WT_0_2 changed to TET_WT_0_2
New Probe Set:2 kb tiles (1362779 probes)
Running windows of size 2000 with step size 2000
Probes Quantitated
Read Count Quantitation using All Reads correcting for total count per million reads log transformed
Looks like PC1 is sparseness of data, and PC2 is level of hydroxy.
Random example regions to show sparseness (apart from the data store report)
some samples have considerable amounts of duplication
Annotation Sets Added
Added 4 annotation sets paradigm_ES_enhancer_tiles_210507.txt - 19377 features paradigm_Epi_enhancer_tiles_210507.txt - 4157 features paradigm_constitutive_bivalent_enhancer_tiles_210507.txt - 772 features paradigm_constitutive_enhancer_tiles_210507.txt - 19049 features
New Probe Set:paradigm enhancers (43355 probes)
Feature generator using paradigm_constitutive_bivalent_enhancer paradigm_constitutive_enhancer paradigm_Epi_enhancer paradigm_ES_enhancer duplicates removed Over feature from 0-0
Probes Quantitated
Read Count Quantitation using All Reads correcting for total count per million reads log transformed
Annotation Sets Added
Added 1 annotation set paradigm enhancers - 43355 features
Exported annotated probe report
