update to proper markdown

Author: kcotto

docs/commands/cis-splice-effects-identify.md

@@ -1,12 +1,15 @@
 [csei]: ../images/csei_examples.png
 
-###Synopsis
+# Overview of `cis-splice-effects identify` command
+
 The `cis-splice-effects identify` command is used to identify splicing misregulation events. This command takes in a list of variants in the VCF format and RNAseq alignments produced with a splice-aware aligner in the BAM format. The tool then proceeds to identify non-canonical splicing junctions near the variant sites.
 
-###Usage
+## Usage
+
 `regtools cis-splice-effects identify [options] variants.vcf alignments.bam ref.fa annotations.gtf`
 
-###Input
+## Input
+
 | Input                  | Description |
 | ------                 | ----------- |
 | variants.vcf | Variant call in VCF format from which to look for cis-splice-effects.|
@@ -16,23 +19,26 @@ The `cis-splice-effects identify` command is used to identify splicing misregula
 
 **Note** - Please make sure that the version of the annotation GTF that you use corresponds with the version of the assembly build (ref.fa) and that the co-ordinates in the VCF file are also from the same build.
 
-###Options
+## Options
+
 | Option  | Description |
 | ------  | ----------- |
-| -o STR	|	Output file containing the aberrant splice junctions with annotations. [STDOUT]	|
-| -v STR	|	Output file containing variants annotated as splice relevant (VCF format).	|
-| -j STR	|	Output file containing the aberrant junctions in BED12 format.	|
-| -s INT	|	Strand specificity of RNA library preparation, where 0 = unstranded/XS, 1 = first-strand/RF, 2 = second-strand/FR. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. If you are unsure, we have created this [table](https://rnabio.org/module-09-appendix/0009/12/01/StrandSettings/) to help. |
-| -w INT	|	Window size in b.p to identify splicing events in. The tool identifies events in variant.start +/- w basepairs. Default behaviour is to look at the window between previous and next exons.	|
-| -e INT	|	Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in exonic space, i.e a coding variant. [3]	|
-| -i INT	|	Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in intronic space. [2]	|
-| -I	|	Annotate variants in intronic space within a transcript(not to be used with -i).	|
-| -E	|	Annotate variants in exonic space within a transcript(not to be used with -e).	|
-| -S	|	Don't skip single exon transcripts.	|
-
-###Output
+| -o STR    |    Output file containing the aberrant splice junctions with annotations. [STDOUT]    |
+| -v STR    |    Output file containing variants annotated as splice relevant (VCF format).    |
+| -j STR    |    Output file containing the aberrant junctions in BED12 format.    |
+| -s INT    |    Strand specificity of RNA library preparation, where 0 = unstranded/XS, 1 = first-strand/RF, 2 = second-strand/FR. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. If you are unsure, we have created this [table](https://rnabio.org/module-09-appendix/0009/12/01/StrandSettings/) to help. |
+| -w INT    |    Window size in b.p to identify splicing events in. The tool identifies events in variant.start +/- w basepairs. Default behaviour is to look at the window between previous and next exons.    |
+| -e INT    |    Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in exonic space, i.e a coding variant. [3]    |
+| -i INT    |    Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in intronic space. [2]    |
+| -I    |    Annotate variants in intronic space within a transcript(not to be used with -i).    |
+| -E    |    Annotate variants in exonic space within a transcript(not to be used with -e).    |
+| -S    |    Don't skip single exon transcripts.    |
+
+## Output
+
 For an explanation of the annotated junctions that are identified by this command please refer to the output of the `junctions annotate` command [here](junctions-annotate.md#output)
 For an explanation of the annotated variants that are identified by this command when using the -v option, please refer to the output of the `variants annotate` command [here](variants-annotate.md#output)
 
-###Examples
+## Examples
+
 ![cis-splice-effects identify example][csei]

docs/commands/junctions-extract.md

@@ -1,15 +1,19 @@
-###Synopsis
+# Overview of `junctions extract` command
+
 The `junctions extract` command can be used to extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format. We have tested this command with alignments from TopHat and by comparing the exon-exon junctions with the `junctions.bed` file produced from TopHat.
 
-###Usage
+## Usage
+
 `regtools junctions extract [options] indexed_alignments.bam`
 
-###Input
+## Input
+
 | Input                  | Description |
 | ------                 | ----------- |
 | indexed_alignments.bam | Aligned RNAseq BAM which has been indexed for example with `samtools index`. We have tested this command with alignments from TopHat.|
 
-###Options
+## Options
+
 | Option  | Description |
 | ------  | ----------- |
 | -a      | Minimum anchor length. 8bp by default. Junctions having a minimum overlap of this much on both ends are reported. Note - the required overlap can be observed amongst separate reads, for example one read might have sufficient left overlap and another read might have sufficient right overlap, this is sufficient for the junction to be reported. No mismatches are allowed in the anchor regions.|
@@ -20,7 +24,8 @@ The `junctions extract` command can be used to extract exon-exon junctions from
 | -h      | Display help message for this command.|
 | -s      | Strand specificity of RNA library preparation, where 0 = unstranded/XS, 1 = first-strand/RF, 2 = second-strand/FR. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. If you are unsure, we have created this [table](https://rnabio.org/module-09-appendix/0009/12/01/StrandSettings/) to help.
 
-###Output
+## Output
+
 The output is in the BED12 format which is described in detail [here.](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) Each line is an exon-exon junction as explained below.
 
 | Column-name       | Description |