formatting

Author: liefeld

docs/v1/index.md

@@ -40,7 +40,9 @@ Finally, compare seqs collapses on binding sites that appear in the same locatio
     - Tab-separated file containing at least two DNA sequences to be analyzed. We suggest only inputting the alignment +/- 15 bp from where the genetic variation of interest occurs. if this is a SNV, you would simply input the 30bp window of the alignment containing the variant. If this is a deletion, you would add 15 bp upstream of the first “-” and 15bp downstream of the last “-”. 
 - **enhancer functional group table (.tsv)**<span style="color: red;">*</span>
     - Tab-separated file which labels each functional group. Functional group can be either wild-type, control, test, or na. If “na”, all enhancers associated with that label will be removed from the analysis. Binding sites are searched for within the “test” group that are not present within the “wild-type” or “control” group. At a minimum both of these requirements must be met, (1) at least one “control” or “wild-type” must be provided; (2) at least one “test” must be provided.
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 <span style="color: red;">*</span>**Either tf affinity information (.tsv) or motif input file (JASPAR format) or both must be provided.**
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 - **tf affinity information (.tsv)**
     -   File containing  all the information for the transcription factors being analyzed, including its name, binding site definition, desired color on the plot, any PBM relative affinity data, and any PFM relative score data. 
 - **motif input file (JASPAR format)**