Update LiftOn documentation: adding bigBed conversion guidance

docs/source/content/bigbed_conversion.rst

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+.. _output_files:
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+bigBed conversion
+=====================
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+To enhance the accessibility and usability of LiftOn's output, converting GFF3 files into the bigBed format is highly recommended. The bigBed format is designed for fast, web-based data streaming and is supported by modern genome browsers such as UCSC Genome Browser, Ensembl, and IGV. This enables users to load data directly through stable links, eliminating the need to download large files or perform manual conversions. This streamlined approach simplifies visualization, facilitates collaboration, and ensures efficient data handling with compressed and indexed files for faster performance when querying genomic regions. By addressing the limitations of GFF3 files, bigBed aligns data sharing practices with current genomic standards and provides an improved experience for users.
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+pre-generated bigBed files
+--------------------------
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+* Human *GRCh38* to *T2T-CHM13*: `<ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/human_refseq/UCSC_genome_browser/lifton.bb>`_
+* Mouse: `<ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/mouse/UCSC_genome_browser/lifton.bb>`_
+* Honeybee: `<ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/bee/UCSC_genome_browser/lifton.bb>`_
+* Thale cress: `<ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/arabadop/UCSC_genome_browser/lifton.bb>`_
+* Rice: `<ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/rice/UCSC_genome_browser/lifton.bb>`_
+* Human *GRCh38* to chimpanzee *panTro6*: `<ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/cross_species/human_to_chimp/UCSC_genome_browser/lifton.bb>`_
+* *Drosophila melanogaster* to *Drosophila erecta*: `<ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/cross_species/drosophila_erecta/UCSC_genome_browser/lifton.bb>`_
+* Mouse to rat: `<ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/cross_species/mouse_to_rat/UCSC_genome_browser/lifton.bb>`_
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+The bigBed format is optimized for fast, web-based data streaming and is universally supported by modern genome browsers like the UCSC Genome Browser. If you would like to use the UCSC Track Hub, please refer to the quick start guide: `UCSC Track Hub guide <https://genome.ucsc.edu/goldenPath/help/hubQuickStartSearch.html>`_.
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+.. image:: ../_images/jhu-logo-dark.png
+   :alt: My Logo
+   :class: logo, header-image only-light
+   :align: center
+
+.. image:: ../_images/jhu-logo-white.png
+   :alt: My Logo
+   :class: logo, header-image only-dark
+   :align: center

docs/source/content/close_species_liftover/liftover_GRCh38_2_chimp.rst

@@ -71,7 +71,7 @@ After successfully running LiftOn, you will get the following file and output di
 
        *  `score.txt <ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/human_to_chimp/lifton_output/score.txt>`_
 
-    3. We also convert the LiftOn annotation GFF3 file into BigBed format, allowing users to load the annotation into the UCSC Genome Browser: /ccb/salz7-data/ftp.ccb/pub/data/LiftOn/human_to_chimp/UCSC_genome_browser/. 
+    3. We also convert the LiftOn annotation GFF3 file into BigBed format, allowing users to load the annotation into the UCSC Genome Browser: ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/human_to_chimp/UCSC_genome_browser/. 
 
        * USCU Track Hub quick start guide: `UCSC Track Hub <https://genome.ucsc.edu/goldenPath/help/hubQuickStartSearch.html>`_
 

docs/source/content/same_species_liftover/liftover_GRCh38_2_T2TCHM13.rst

@@ -75,7 +75,7 @@ After successfully running LiftOn, you will get the following file and output di
 
        *  `score.txt <ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/human_refseq/lifton_output/score.txt>`_
 
-    3. We also convert the LiftOn annotation GFF3 file into BigBed format, allowing users to load the annotation into the UCSC Genome Browser: /ccb/salz7-data/ftp.ccb/pub/data/LiftOn/human_refseq/UCSC_genome_browser/. 
+    3. We also convert the LiftOn annotation GFF3 file into BigBed format, allowing users to load the annotation into the UCSC Genome Browser: ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/human_refseq/UCSC_genome_browser/. 
 
        * USCU Track Hub quick start guide: `UCSC Track Hub <https://genome.ucsc.edu/goldenPath/help/hubQuickStartSearch.html>`_
 

docs/source/index.rst

@@ -216,6 +216,7 @@ Table of contents
     :maxdepth: 2
 
     content/output_explanation
+    content/bigbed_conversion
     content/feature_counting
     content/evaluation_metrics
     content/behind_scenes