fix links

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@@ -75,13 +76,13 @@ Sequence files are from unpublished results and currently unavailable.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.
 
 

docs/DeDuplicationEvaluation/H3K4Me3_results.md

@@ -15,23 +15,23 @@ 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
 
 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
 
 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

docs/DeDuplicationEvaluation/RNAPol2_results.md

@@ -19,23 +19,23 @@ 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
 
 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
 
 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

docs/DeDuplicationEvaluation/TF_results.md

@@ -20,23 +20,23 @@ 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
 
 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
 
 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