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index.Rmd
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---
output:
html_document:
toc: true
---
<h1 style="color:grey;font-family:arial; position:relative; top:15px;text-align:center;">Collaboration J project<img src="website_materials/research_website_logo.png" style="float:right;width:200px;height:150px;"></h1>
<br>
***
### 0. **Available data set**
* Project data list shared in Google drive [Click...](https://drive.google.com/open?id=1WesFCQTrFplnXRKCHmhqtm1529DHc5Sc2tX7GkRa_-U).
<br>
### 1. **spike-in distribution**
* 161116 1-site,2-site,and negative control, stringent mapping, PCR duplicates removed [[More...]](./analysis/161120_161116_spike_in_data_plot_reads_distribution.html).
* 160917_160811 1-site spike-in, mapping allowing for mismatches, PCR duplicates removed [[More...]](./analysis/160912_plot_reads_distribution_UMI_dedupped.html).
* 170120_first, mapping not allowing for mismatches, PCR duplicates removed [[More...]](./analysis/170204_170120_first_batch_spike_in_plot_reads_distribution.html).
* 170321, using one positive control sequence and two negative control sequence [[More...]](./analysis/170330_20170321_spike_in_analysis.html).
<br>
### 2. **Real data distribution**
* 160912_160620, compared to Tab-Seq all peaks, mapping allowing mismatches, PCR duplicates removed [[More...]](./analysis/160912_plot_reads_distribution_UMI_dedupped.html).
* 161120_160620, compared to Tab-Seq FDR 0.484 peaks, mapping allowing mismatches, PCR duplicates removed [[More...]](./analysis/161120_160620_data_plot_reads_distribution.html).
* 170120_first data, compared to Tab-Seq FDR 0.484 peaks, mapping not allowing mismatches, PCR duplicates removed [[More...]](./analysis/170204_170120_first_batch_data_plot_reads_distribution.html).
<br>
### 3. **Shengtong peak overlap analysis**
* drop_box_share made by Shengtong Han [[More...]](./analysis/JumpSeq_dropbox_shengtong.pdf).
<br>
### 4. **Paired end sequencing analysis**
* 161218 analysis pipeline [[More...]](./analysis/161218_paired_end_reads_mapping_pipeline.html).
* 161218 pipeline, 20161130 5hmc data, processed reads number and mappable reads number [[More...]](./analysis/161218_161130_paired_end_reads_statistics.html).
* 161218 pipeilne, 20161130 5mc data, processed reads number and mapped reads number [[More...]](./analysis/161222_161130_5mc_paired_end_reads_statistics.html).
* 161218 pipeline, 20170110 5mc data, processed reads number and mapped reads number [[More...]](./analysis/170115_170110_paired_end_reads_statistics.html).
<br>
### 5. **distinct reads Saturation analysis**
* 161226 analysis for all previous 5hmc 48 ng data and one 2.4 ng data [[More...]](./analysis/161226_previous_5hmc_distinct_reads_saturation_analysis.html)
<br>
### 6. **Investigation on reads lost at each preprocessing step**
* Investiage reads lost at each step for all previous up to 160811 48ng 5hmc data [[More...]](./analysis/170207_previous_5hmc_samples_reads_lost_at_each_preprocessing_step.html).
* Explore why there is a low mappability rate for reads with a Jump-Seq barcode. Use 160402 5hmc data (He-lu-6_S6_L006_R1_001). Randomly picked 10 reads, 6 reads have multiple alignments, 6 reads would have been mapped if allowing for 2 or 3 mismatches, 3 reads are not mapped even if allowing for 3 mismatches [[More...]](./analysis/170210_investigate_low_mappability_issue.html).
* 170120_second, cell free DNA Jump-Seq (323T_hmC_jump_cfDNA) reads statistics at each step [[More...]](./analysis/170210_20170120_second_human_cf_5hmc_samples_reads_lost_at_each_preprocessing_step.html).
* 170321 5hmc data, from a protocol that is supposed to reduce the sequencing array and to have more distinct reads [[More...]](./analysis/170330_20170321_5hmc_samples_reads_lost_at_each_preprocessing_step.html).
* Reads lost at each step for all 0.6ng 5hmc Jump-Seq data [[More...]](./analysis/170407_0.6ng_5hmc_samples_reads_lost_at_each_preprocessing_step.html).
<br>
### 7. Peaks compariosn
* compare gDNA hmc seal peaks from tumor samples to from adjacent tissues. Also compare cell-free DNA hmc seal sites with these sites [[More...]](./analysis/170210_20170120_second_human_cf_5hmc_samples_peak_comparison.html).
* Plot 5'ends of 5hmc reads on mES p300 peaks [[More...]](./analysis/170309_5hmc_reads_coverage_on_peaks.html).
* Reads coverage comparion between rep1 and rep2 on 1kb windows enriched for pooled 5hmc Jump-Seq reads (pooled from 11 replicates) [[More..]](./analysis/170410_big_rep1_rep2_reads_coverage_in_1kb_enriched_windows.html).
* Compare 0.6ng 5hmc Jump-Seq read 5' ends with 1kb windows enriched for pooled 5hmc Jump-Seq reads (pooled from 11 replicates) [[More...]](./analysis/170410_0.6ng_5hmc_reads_overlap_with_48ng_peaks.html).
***
**Last updated:** `r Sys.time()`