Update README.md

README.md

@@ -9,7 +9,7 @@ The main program `CIRIdeep.py` can be used to predict differentially spliced cir
 
 **Prediction with CIRIdeep using total RNA-seq data**
 
-CIRIdeep provides probability of given circRNAs being differentially spliced between any of two samples. When predict with CIRIdeep, expression value of 1499 RBPs (listed in `./demo/RBPmax_totalRNA.tsv`) and splicing amount (derived from SAM alignment files) in both samples are needed. The order of RBP expression of each sample should keep exactly the same with `RBP max value file`. We recommend to process raw total RNA-seq raw fastq files with `CIRIquant`, which provides junction ratio of each circRNA and expression value of each gene in a one-stop manual. SAM files generated with BWA is recommended when producing splicing amount values.
+CIRIdeep provides probability of given circRNAs being differentially spliced between any of two samples. When predict with CIRIdeep, expression value of 1499 RBPs (listed in `./demo/RBPmax_totalRNA.tsv`) and splicing amount (derived from SAM alignment files) in both samples are needed. The order of RBP expression of each sample should keep exactly the same with `RBP max value file`. We recommend to process raw total RNA-seq fastq files with `CIRIquant`, which provides junction ratio of each circRNA and expression value of each gene in a one-stop manual. SAM files generated with BWA is recommended when producing splicing amount values.
 
 ```
 python CIRIdeep.py predict -geneExp_absmax ./demo/RBPmax_totalRNA.tsv -seqFeature ./demo/cisfeature.tsv -splicing_max ./demo/splicingamountmax_max.tsv -predict_list ./demo/predict_list.txt -model_path ./model/CIRIdeep.h5 -outdir ./outdir -RBP_dir ./demo/RBPexp_total -splicing_dir ./demo/splicingamount
@@ -37,6 +37,7 @@ CircRNAs are given as coodination on `hg19` genome, like `chr10:102683732|102685
 **Prediction with CIRIdeep(A) using poly(A) selected RNA-seq data**
 
 CIRIdeep(A) gives three probabilities indicating the circRNA being unchanged, having higher junction ratio in sample A or having higher junction ratio in sample B, which sum to one.
+Order of samples (A, B) is the same with sample pair name given in  `predict list file`.
 As in some cases, like in scRNA-seq or spatial transcriptomics data, only gene expression matrix is provided, splicing amount is not needed in CIRIdeep(A) any more.
 
 ```