From 0186fbce757e6ceb830d10f9b73bc31f44898381 Mon Sep 17 00:00:00 2001 From: Timothy Parnell Date: Fri, 1 Nov 2024 11:50:45 -0600 Subject: [PATCH] fix links --- docs/DeDuplicationEvaluation/DeDuplication.md | 19 ++++++++++--------- .../H3K4Me3_results.md | 8 ++++---- .../RNAPol2_results.md | 8 ++++---- docs/DeDuplicationEvaluation/TF_results.md | 8 ++++---- 4 files changed, 22 insertions(+), 21 deletions(-) diff --git a/docs/DeDuplicationEvaluation/DeDuplication.md b/docs/DeDuplicationEvaluation/DeDuplication.md index 75c2772..f36e862 100644 --- a/docs/DeDuplicationEvaluation/DeDuplication.md +++ b/docs/DeDuplicationEvaluation/DeDuplication.md @@ -46,12 +46,13 @@ application from the Reads were aligned to the genome using Novocraft Novoalign (version 4.3). Alignment bam files were processed with either -[bam_partial_dedup.pl](applications/bam_partial_dedup) or with -[bam_umi_dedup.pl](https://huntsmancancerinstitute.github.io/UMIScripts/apps/bam_umi_dedup.html) from the [UMIScripts -package](https://huntsmancancerinstitute.github.io/UMIScripts/). With partial -de-duplication, all optical duplicates (optical threshold of 2500 pixels) were -completely removed. Exclusion peaks, identified from the corresponding Input, were -called (without prior de-duplication) and used to exclude alignments in all cases. +[bam_partial_dedup.pl](../applications/bam_partial_dedup) or with +[bam_umi_dedup.pl](https://huntsmancancerinstitute.github.io/UMIScripts/apps/bam_umi_dedup.html) +from the [UMIScripts package](https://huntsmancancerinstitute.github.io/UMIScripts/). +With partial de-duplication, all optical duplicates (optical threshold of 2500 +pixels) were completely removed. Exclusion peaks, identified from the corresponding +Input, were called (without prior de-duplication) and used to exclude alignments in +all cases. Six different permutations were generated and compared. Labels are with respect to the number of duplicates retained. @@ -75,13 +76,13 @@ Sequence files are from unpublished results and currently unavailable. Several plots are provided here as generated by the pipeline. -See [H3K4Me3 results](DeDuplicationEvaluation/H3K4Me3_results.md) for a high +See [H3K4Me3 results](H3K4Me3_results.md) for a high occurrence, high occupancy factor. -See [RNA Polymerase II results](DeDuplicationEvaluation/RNAPol2_results.md) for a +See [RNA Polymerase II results](RNAPol2_results.md) for a very high occurrence, moderate occupancy factor. -See [Transcription Factor results](DeDuplicationEvaluation/TF_results.md) for a low +See [Transcription Factor results](TF_results.md) for a low occurrence, low occupancy factor. diff --git a/docs/DeDuplicationEvaluation/H3K4Me3_results.md b/docs/DeDuplicationEvaluation/H3K4Me3_results.md index 3858d40..187e6ee 100644 --- a/docs/DeDuplicationEvaluation/H3K4Me3_results.md +++ b/docs/DeDuplicationEvaluation/H3K4Me3_results.md @@ -15,7 +15,7 @@ The number of peaks called between different subsets were nearly identical. Usin alignments called the most number of peaks. The mean peak length was 1568 ± 1140 bp, median 1350 bp at a threshold q-value of 2. -![H3K4me3_peak_number](DeDuplicationEvaluation/H3K4me3.peak_number.png) +![H3K4me3_peak_number](H3K4me3.peak_number.png) ### ChIP Efficiency @@ -23,7 +23,7 @@ median 1350 bp at a threshold q-value of 2. The fraction of alignments within the respectively called peaks was quite good, with nearly identical fractions between the subsets, ranging from 43-45%. -![H3K4me3_chip_efficiency](DeDuplicationEvaluation/H3K4me3.chip_efficiency.png) +![H3K4me3_chip_efficiency](H3K4me3.chip_efficiency.png) ### Peak Fragment Coverage Profile @@ -31,7 +31,7 @@ nearly identical fractions between the subsets, ranging from 43-45%. The depth-normalized fragment coverage profile over the called peak midpoint ± 1 Kb shows no difference between the subsets. -![H3K4me3_profile_fragment](DeDuplicationEvaluation/H3K4me3_profile_fragment_hm.png) +![H3K4me3_profile_fragment](H3K4me3_profile_fragment_hm.png) ### Comparison of Duplicate Alignments Within Peaks @@ -47,7 +47,7 @@ duplicate alignments found within peaks. Notably, however, the difference is onl few percentage points, and more importantly, very little with UMI-deduplicated alignments. -![H3K4me3_efficiency_comparison](DeDuplicationEvaluation/H3K4me3_comparison.chip_efficiency.png) +![H3K4me3_efficiency_comparison](H3K4me3_comparison.chip_efficiency.png) ### Conclusion diff --git a/docs/DeDuplicationEvaluation/RNAPol2_results.md b/docs/DeDuplicationEvaluation/RNAPol2_results.md index 05a8b12..b1b3c81 100644 --- a/docs/DeDuplicationEvaluation/RNAPol2_results.md +++ b/docs/DeDuplicationEvaluation/RNAPol2_results.md @@ -19,7 +19,7 @@ retained duplicates. The mean peak length was 1140 ± 1883 bp, median 635 bp at a threshold q-value of 2. -![RNAPol2_peak_number](DeDuplicationEvaluation/RNAPol2.peak_number.png) +![RNAPol2_peak_number](RNAPol2.peak_number.png) ### ChIP Efficiency @@ -27,7 +27,7 @@ The mean peak length was 1140 ± 1883 bp, median 635 bp at a threshold q-value o The fraction of alignments within the respectively called peaks was quite good, with nearly identical fractions between the subsets, ranging from 33-35%. -![RNAPol2_chip_efficiency](DeDuplicationEvaluation/RNAPol2.chip_efficiency.png) +![RNAPol2_chip_efficiency](RNAPol2.chip_efficiency.png) ### Peak Fragment Coverage Profile @@ -35,7 +35,7 @@ nearly identical fractions between the subsets, ranging from 33-35%. The depth-normalized fragment coverage profile over the called peak midpoint ± 1 Kb shows no difference between the subsets. -![RNAPol2_profile_fragment](DeDuplicationEvaluation/RNAPol2_profile_fragment_hm.png) +![RNAPol2_profile_fragment](RNAPol2_profile_fragment_hm.png) ### Comparison of Duplicate Alignments Within Peaks @@ -51,7 +51,7 @@ duplicate alignments found within peaks. Notably, however, the difference is onl few percentage points, and more importantly, very little with UMI-deduplicated alignments. -![RNAPol2_efficiency_comparison](DeDuplicationEvaluation/RNAPol2_comparison.chip_efficiency.png) +![RNAPol2_efficiency_comparison](RNAPol2_comparison.chip_efficiency.png) ### Conclusion diff --git a/docs/DeDuplicationEvaluation/TF_results.md b/docs/DeDuplicationEvaluation/TF_results.md index c74e85f..44a1930 100644 --- a/docs/DeDuplicationEvaluation/TF_results.md +++ b/docs/DeDuplicationEvaluation/TF_results.md @@ -20,7 +20,7 @@ Leaving in all duplicates calls nearly 40% more peaks. The mean peak length was 418 ± 182 bp, median 370 bp at a threshold q-value of 2. -![TF_peak_number](DeDuplicationEvaluation/TF.peak_number.png) +![TF_peak_number](TF.peak_number.png) ### ChIP Efficiency @@ -28,7 +28,7 @@ The mean peak length was 418 ± 182 bp, median 370 bp at a threshold q-value of The fraction of alignments within the respectively called peaks was quite low, as expected for such few peak numbers called, ranging from 0.25% to 0.30%. -![TF_chip_efficiency](DeDuplicationEvaluation/TF.chip_efficiency.png) +![TF_chip_efficiency](TF.chip_efficiency.png) ### Peak Fragment Coverage Profile @@ -36,7 +36,7 @@ expected for such few peak numbers called, ranging from 0.25% to 0.30%. The depth-normalized fragment coverage profile over the called peak midpoint ± 1 Kb shows no difference between the subsets. -![TF_profile_fragment](DeDuplicationEvaluation/TF_profile_fragment_hm.png) +![TF_profile_fragment](TF_profile_fragment_hm.png) ### Comparison of Duplicate Alignments Within Peaks @@ -51,7 +51,7 @@ the peaks than completely deduplicated alignments, indicating there are indeed duplicate alignments found within peaks. Notably, however, the difference is quite small. -![TF_efficiency_comparison](DeDuplicationEvaluation/TF_comparison.chip_efficiency.png) +![TF_efficiency_comparison](TF_comparison.chip_efficiency.png) ### Conclusion