update README.md

README.md

@@ -1,29 +1,21 @@
-### Choppy APP Usage
-$ open-choppy-env
-$ choppy install YaqingLiu/bamdst
-$ choppy batch YaqingLiu/bamdst-latest samples.csv -p project_name
-
-### samples.csv
-sample_id,sample,bam,bed
-
-
-### bamdst -- a BAM Depth Stat Tool
+## bamdst -- a BAM Depth Stat Tool
 
 Bamdst is a lightweight tool to stat the depth coverage of  target regions of bam file(s).
 
-Bam file(s) should be properly sorted, and the probe file (bed file) and the output dir
+Bam file(s) should be properly sorted, and the probe file (bed file) and the output dir must be specified in the first place.
 
-must be specified in the first place.
 
-#### USAGE
+#### Choppy APP Usage
+    open-choppy-env
+    choppy install YaqingLiu/bamdst
+    choppy batch YaqingLiu/bamdst-latest samples.csv -p project_name
 
-Normal:
+-**samples.csv**
+    sample_id,sample,bam,bed
 
+-**bamdst normal usage:**
     bamdst -p <probe.bed> -o ./ in1.bam
 
-Pipeline mode:
-
-    samtools view in1.bam -u | bamdst -p x.bed -o ./ -
 
 #### PARAMETERS
 
@@ -35,6 +27,7 @@ set the output dir [mandatory]
 
 the probe or captured target region file, these regions will be merged first [mandatory]
 
+
 #### OUTPUT FILES
 
 Seven files will be created in the output direction. There are:
@@ -53,13 +46,12 @@ Seven files will be created in the output direction. There are:
 
 -**uncover.bed**
 
+
 #### DETAILS of each file
 
 **coverage.report**
 
-This file contains all the coverage information of target and
-
-flank region, and reads stat information of the input file(s). 
+This file contains all the coverage information of target and flank region, and reads stat information of the input file(s). 
 
 Here is the full details of each entry.
 
@@ -141,43 +133,16 @@ Depth and coverage information of each chromosome.
 
 **region.tsv.gz**
 
-For each region in probe file (in.bed), average depth, median
-
-depth and coverage of these regions will be listed in the file.
+For each region in probe file (in.bed), average depth, median depth and coverage of these regions will be listed in the file.
 
 **depth.tsv.gz**
 
-For each position in the probe file(in.bed), three kinds depth
-
-value will be calculated, including raw depth, rmdup depth and
-
-the coverage depth. The raw depth is retrieved from input bam 
-
-file(s) without any restriction. And the rmdup depth is 
-
-calculated after remove duplicated reads and secondary alignment
-
-reads and low map quality reads(mapQ < 20), this value is similar
-
-with the output depth of `samtools depth`. The coverage depth is
-
-the raw depth with consider of deletion region, so this value 
-
-should be equal to or greated than the raw depth. We usw raw depth
-
-to stat the coverage information in the coverage.report file. If
-
-you want use rmdup depth to calculate the coverage, please use 
-
-the parameter "--use_rmdup".
+For each position in the probe file(in.bed), three kinds depth value will be calculated, including raw depth, rmdup depth and the coverage depth. The raw depth is retrieved from input bam file(s) without any restriction. And the rmdup depth is calculated after remove duplicated reads and secondary alignment reads and low map quality reads(mapQ < 20), this value is similar with the output depth of `samtools depth`. The coverage depth is the raw depth with consider of deletion region, so this value should be equal to or greated than the raw depth. We usw raw depth to stat the coverage information in the coverage.report file. If you want use rmdup depth to calculate the coverage, please use the parameter "--use_rmdup".
 
 **uncover.bed**
 
-This bed file contains the bad covered or uncovered region in the
-
-input bam file(s) against the probe file. Set the cutoff value of
+This bed file contains the bad covered or uncovered region in the input bam file(s) against the probe file. Set the cutoff value of uncover by parameter "--uncover"
 
-uncover by parameter "--uncover"
 
 #### Known bugs