Teichlab
diff --git a/‎data/3M-february-2018.txt.gz ‎data/10X-Genomics/3M-february-2018.txt.gz b/‎data/3M-february-2018.txt.gz ‎data/10X-Genomics/3M-february-2018.txt.gz
diff --git a/‎data/737K-april-2014_rc.txt.gz ‎data/10X-Genomics/737K-april-2014_rc.txt.gz b/‎data/737K-april-2014_rc.txt.gz ‎data/10X-Genomics/737K-april-2014_rc.txt.gz
diff --git a/‎data/737K-august-2016.txt.gz ‎data/10X-Genomics/737K-august-2016.txt.gz b/‎data/737K-august-2016.txt.gz ‎data/10X-Genomics/737K-august-2016.txt.gz
diff --git a/‎data/737K-cratac-v1.txt.gz ‎data/10X-Genomics/737K-cratac-v1.txt.gz b/‎data/737K-cratac-v1.txt.gz ‎data/10X-Genomics/737K-cratac-v1.txt.gz
diff --git a/‎data/CG000108_AssayConfiguration_SC3v2.pdf ‎data/10X-Genomics/CG000108_AssayConfiguration_SC3v2.pdf b/‎data/CG000108_AssayConfiguration_SC3v2.pdf ‎data/10X-Genomics/CG000108_AssayConfiguration_SC3v2.pdf
diff --git a/‎data/CG000109_AssayConfiguration_VDJ_RevD.pdf ‎data/10X-Genomics/CG000109_AssayConfiguration_VDJ_RevD.pdf b/‎data/CG000109_AssayConfiguration_VDJ_RevD.pdf ‎data/10X-Genomics/CG000109_AssayConfiguration_VDJ_RevD.pdf
diff --git a/‎data/CG000168_ChromiumSingleCellATAC_ReagentKits_UserGuide_RevA.pdf ‎data/10X-Genomics/CG000168_ChromiumSingleCellATAC_ReagentKits_UserGuide_RevA.pdf b/‎data/CG000168_ChromiumSingleCellATAC_ReagentKits_UserGuide_RevA.pdf ‎data/10X-Genomics/CG000168_ChromiumSingleCellATAC_ReagentKits_UserGuide_RevA.pdf
diff --git a/‎data/CG000183_ChromiumSingleCell3__v3_UG_Rev-A.pdf ‎data/10X-Genomics/CG000183_ChromiumSingleCell3__v3_UG_Rev-A.pdf b/‎data/CG000183_ChromiumSingleCell3__v3_UG_Rev-A.pdf ‎data/10X-Genomics/CG000183_ChromiumSingleCell3__v3_UG_Rev-A.pdf
diff --git a/‎data/CG000184_ChromiumSingleCellSingleCell3v3_FeatureBarcodingtechnology_CRISPR_RevA.pdf ‎data/10X-Genomics/CG000184_ChromiumSingleCellSingleCell3v3_FeatureBarcodingtechnology_CRISPR_RevA.pdf b/‎data/CG000184_ChromiumSingleCellSingleCell3v3_FeatureBarcodingtechnology_CRISPR_RevA.pdf ‎data/10X-Genomics/CG000184_ChromiumSingleCellSingleCell3v3_FeatureBarcodingtechnology_CRISPR_RevA.pdf
diff --git a/‎data/CG000185_ChromiumSingleCell3__FeatureBarcode_CellSurfaceProtein_RevA.pdf ‎data/10X-Genomics/CG000185_ChromiumSingleCell3__FeatureBarcode_CellSurfaceProtein_RevA.pdf b/‎data/CG000185_ChromiumSingleCell3__FeatureBarcode_CellSurfaceProtein_RevA.pdf ‎data/10X-Genomics/CG000185_ChromiumSingleCell3__FeatureBarcode_CellSurfaceProtein_RevA.pdf
diff --git a/‎data/CG000185_ChromiumSingleCell3__FeatureBarcode_CellSurfaceProtein_Rev_B.pdf ‎data/10X-Genomics/CG000185_ChromiumSingleCell3__FeatureBarcode_CellSurfaceProtein_Rev_B.pdf b/‎data/CG000185_ChromiumSingleCell3__FeatureBarcode_CellSurfaceProtein_Rev_B.pdf ‎data/10X-Genomics/CG000185_ChromiumSingleCell3__FeatureBarcode_CellSurfaceProtein_Rev_B.pdf
diff --git a/‎data/CG000197_GuideRNA_SpecificationsCompatible_withFeatureBarcodingtechnology_forCRISPRScreening_Rev-A.pdf ‎data/10X-Genomics/CG000197_GuideRNA_SpecificationsCompatible_withFeatureBarcodingtechnology_forCRISPRScreening_Rev-A.pdf b/‎data/CG000197_GuideRNA_SpecificationsCompatible_withFeatureBarcodingtechnology_forCRISPRScreening_Rev-A.pdf ‎data/10X-Genomics/CG000197_GuideRNA_SpecificationsCompatible_withFeatureBarcodingtechnology_forCRISPRScreening_Rev-A.pdf
diff --git a/‎data/CG00026_Chromium_Single_Cell_3__Reagent_Kits_User_Guide_RevB.PDF ‎data/10X-Genomics/CG00026_Chromium_Single_Cell_3__Reagent_Kits_User_Guide_RevB.PDF b/‎data/CG00026_Chromium_Single_Cell_3__Reagent_Kits_User_Guide_RevB.PDF ‎data/10X-Genomics/CG00026_Chromium_Single_Cell_3__Reagent_Kits_User_Guide_RevB.PDF
diff --git a/‎data/CG000330_ChromiumNextGEMSingleCell5_v2_CellSurfaceProtein_RevA.pdf ‎data/10X-Genomics/CG000330_ChromiumNextGEMSingleCell5_v2_CellSurfaceProtein_RevA.pdf b/‎data/CG000330_ChromiumNextGEMSingleCell5_v2_CellSurfaceProtein_RevA.pdf ‎data/10X-Genomics/CG000330_ChromiumNextGEMSingleCell5_v2_CellSurfaceProtein_RevA.pdf
diff --git a/‎data/sgRNA_purterb_10x_cs_loc1.svg ‎data/10X-Genomics/sgRNA_purterb_10x_cs_loc1.svg b/‎data/sgRNA_purterb_10x_cs_loc1.svg ‎data/10X-Genomics/sgRNA_purterb_10x_cs_loc1.svg
diff --git a/‎data/sgRNA_purterb_10x_cs_loc2.svg ‎data/10X-Genomics/sgRNA_purterb_10x_cs_loc2.svg b/‎data/sgRNA_purterb_10x_cs_loc2.svg ‎data/10X-Genomics/sgRNA_purterb_10x_cs_loc2.svg
diff --git a/‎data/translation_3M-february-2018.txt.gz ‎data/10X-Genomics/translation_3M-february-2018.txt.gz b/‎data/translation_3M-february-2018.txt.gz ‎data/10X-Genomics/translation_3M-february-2018.txt.gz
diff --git a/‎docs/source/epi/10x_scATAC-seq.md
+1-1 b/‎docs/source/epi/10x_scATAC-seq.md
+1-1
diff --git a/‎docs/source/ge/10xChromium3v1.md
+1-1 b/‎docs/source/ge/10xChromium3v1.md
+1-1
diff --git a/‎docs/source/ge/10xChromium3v2.md
+1-1 b/‎docs/source/ge/10xChromium3v2.md
+1-1
diff --git a/‎docs/source/ge/10xChromium3v3.md
+1-1 b/‎docs/source/ge/10xChromium3v3.md
+1-1
diff --git a/‎docs/source/ge/10xChromium5.md
+1-1 b/‎docs/source/ge/10xChromium5.md
+1-1
diff --git a/‎docs/source/multi/ISSAAC-seq.md
+1-1 b/‎docs/source/multi/ISSAAC-seq.md
+1-1
diff --git a/‎methods_html/10xChromium3.html
+2-2 b/‎methods_html/10xChromium3.html
+2-2
@@ -129,7 +129,7 @@ The barcodes on the gel beads of the 10x Genomics platform are well defined. We
 ```console
 # download the whitelist
 
-wget -P 10xscATAC/pbmc500/ https://teichlab.github.io/scg_lib_structs/data/737K-cratac-v1.txt.gz
+wget -P 10xscATAC/pbmc500/ https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/737K-cratac-v1.txt.gz
 gunzip 10xscATAC/pbmc500/737K-cratac-v1.txt.gz
 
 # reverse complement the whitelist
 
@@ -275,7 +275,7 @@ The barcodes on the gel beads of the 10x Genomics platform are well defined. We
 
 ```console
 # download the whitelist 
-wget -P zheng2017/data/ https://teichlab.github.io/scg_lib_structs/data/737K-april-2014_rc.txt.gz
+wget -P zheng2017/data/ https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/737K-april-2014_rc.txt.gz
 gunzip zheng2017/data/737K-april-2014_rc.txt.gz
 ```
 
 
@@ -96,7 +96,7 @@ The barcodes on the gel beads of the 10x Genomics platform are well defined. We
 
 ```console
 # download the whitelist 
-wget -P mereu2020/10xV2 https://teichlab.github.io/scg_lib_structs/data/737K-august-2016.txt.gz
+wget -P mereu2020/10xV2 https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/737K-august-2016.txt.gz
 gunzip mereu2020/10xV2/737K-august-2016.txt.gz
 ```
 
 
@@ -98,7 +98,7 @@ The barcodes on the gel beads of the 10x Genomics platform are well defined. We
 
 ```console
 # download the whitelist
-wget -P mereu2020/10xV3 wget https://teichlab.github.io/scg_lib_structs/data/3M-february-2018.txt.gz
+wget -P mereu2020/10xV3 wget https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/3M-february-2018.txt.gz
 gunzip mereu2020/10xV3/3M-february-2018.txt.gz
 ```
 
 
@@ -96,7 +96,7 @@ The barcodes on the gel beads of the 10x Genomics platform are well defined. We
 
 ```console
 # download the whitelist 
-wget -P masuda2022/10x5p https://teichlab.github.io/scg_lib_structs/data/737K-august-2016.txt.gz
+wget -P masuda2022/10x5p https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/737K-august-2016.txt.gz
 gunzip masuda2022/10x5p/737K-august-2016.txt.gz
 ```
 
 
@@ -162,7 +162,7 @@ The barcodes on the gel beads of the 10x Genomics platform are well defined. We
 ```console
 # download the whitelist
 
-wget -P ISSAAC-seq/data https://teichlab.github.io/scg_lib_structs/data/737K-cratac-v1.txt.gz
+wget -P ISSAAC-seq/data https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/737K-cratac-v1.txt.gz
 gunzip ISSAAC-seq/data/737K-cratac-v1.txt.gz
 
 # reverse complement the whitelist
 
@@ -8,9 +8,9 @@
 <body>
 
 <h1><a href="https://support.10xgenomics.com/single-cell-gene-expression" target="_blank"><span style="color:red;">10x Chromium Single Cell 3' Solution V2 and V3</span></a></h1>
-<p><span style="font-size:1.1em;">The Chromium Single Cell 3' Solution V2 chemistry is shown here. Oligo sequence information is taken from <a href="../data/CG000108_AssayConfiguration_SC3v2.pdf" target="_blank"><span style="color:blue;">The 10x Genomics Technical Note</span></a>. You can find out all the cell barcodes (16 bp) here: <a href="../data/737K-august-2016.txt.gz" target="_blank">737K-august-2016.txt.gz</a>. This file is copied from <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger" target="blank">Cell Ranger</a> (using Cell Ranger v2.1.0 as an example) /path/to/cellranger-2.1.0/cellranger-cs/2.1.0/tenkit/lib/python/tenkit/barcodes.</span></p>
+<p><info>The Chromium Single Cell 3' Solution V2 chemistry is shown here. Oligo sequence information is taken from <a href="../data/10X-Genomics/CG000108_AssayConfiguration_SC3v2.pdf" target="_blank"><span style="color:blue;">The 10x Genomics Technical Note</span></a>. You can find out all the cell barcodes (16 bp) here: <a href="../data/10X-Genomics/737K-august-2016.txt.gz" target="_blank">737K-august-2016.txt.gz</a>. This file is copied from <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger" target="blank">Cell Ranger</a> (using Cell Ranger v2.1.0 as an example) /path/to/cellranger-2.1.0/cellranger-cs/2.1.0/tenkit/lib/python/tenkit/barcodes.</info></p>
 
-<p><span style="font-size:1.1em;"><a href="../data/CG000183_ChromiumSingleCell3__v3_UG_Rev-A.pdf" target="_blank">The V3 chemistry</a> gave better sensitivity (detects more genes) comparing to the V2 chemistry. In addition, the oligo beads are modified to support feature barcoding. In terms of the 3' gene expression library preparation, there are only a few nucleotide differences for some oligos. The final library structure is exactly the same, except that the UMI is 10-bp long in V2 but 12-bp in V3. The cell barcodes whitelist for the V3 chemistry can be found here: <a href="../data/3M-february-2018.txt.gz" target="_blank">3M-february-2018.txt.gz</a>. This file is copied from the Cell Ranger software (using Cell Ranger v3.1.0 as an example): cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/3M-february-2018.txt.gz. Oligo sequences are provided for both V2 and V3 if they are different. Only V2 library preparation is drawn here.</span></p>
+<p><info><a href="../data/10X-Genomics/CG000183_ChromiumSingleCell3__v3_UG_Rev-A.pdf" target="_blank">The V3 chemistry</a> gave better sensitivity (detects more genes) comparing to the V2 chemistry. In addition, the oligo beads are modified to support feature barcoding. In terms of the 3' gene expression library preparation, there are only a few nucleotide differences for some oligos. The final library structure is exactly the same, except that the UMI is 10-bp long in V2 but 12-bp in V3. The cell barcodes whitelist for the V3 chemistry can be found here: <a href="../data/10X-Genomics/3M-february-2018.txt.gz" target="_blank">3M-february-2018.txt.gz</a>. This file is copied from the Cell Ranger software (using Cell Ranger v3.1.0 as an example): cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/3M-february-2018.txt.gz. Oligo sequences are provided for both V2 and V3 if they are different. Only V2 library preparation is drawn here.</info></p>
 
 <br>