updated docs

docs/cnvs.md

@@ -44,9 +44,8 @@ Read alignment options (if using --align):
 Quantify genes options (if using --call_genes):
   --readq INT           Discard reads with mean quality < READQ (20)
   --mapid FLOAT         Discard reads with alignment identity < MAPID (94.0)
-  --mapq INT            Discard reads with mapping quality < MAPQ (10)
   --aln_cov FLOAT       Discard reads with alignment coverage < ALN_COV (0.75)
-  --trim INT            Trim N base-pairs from read-tails (0)
+  --trim INT            Trim N base-pairs from 3'/right end of reads (0)
 ```
 
 ## Examples

docs/install.md

@@ -20,7 +20,7 @@ Or, download the latest source code:
 https://github.com/snayfach/MIDAS/archive/master.zip  
 And unpack the project: `unzip MIDAS-master.zip`  
 
-Or, download a stable release of the source code:
+Or, download a stable release of the source code:  
 [https://github.com/snayfach/MIDAS/releases] (https://github.com/snayfach/MIDAS/releases)  
 
 ### Install dependencies
@@ -45,7 +45,7 @@ If you still have installation issues, please open a new [issue] (https://github
 
 This will enable you to run MIDAS scripts:  
 `export PYTHONPATH=$PYTHONPATH:/path/to/MIDAS`  
-`export PATH=$PATH:/path/to/MIDAS/scripts` 
+`export PATH=$PATH:/path/to/MIDAS/scripts`   
 `export MIDAS_DB=/path/to/midas_database` 
 
 Be sure to replace '/path/to' with the appropriate path on your system  

docs/ref_db.md

@@ -12,8 +12,8 @@ on Unix: `wget http://lighthouse.ucsf.edu/MIDAS/midas_db_v1.2.tar.gz`
 on OSX: `curl http://lighthouse.ucsf.edu/MIDAS/midas_db_v1.2.tar.gz > midas_db_v1.2.tar.gz`
 
 * This may take several minutes to several hours, depending on your internet speed
-* The entire database requires 32 GB of free space to download and decompress
-* Once decompressed, it takes 16G of free space
+* The entire database requires 36 GB of free space to download and decompress
+* Once decompressed, it takes 18G of free space
 * See midas_db_v1.2/README for more information
 
 #### Step 2. unpack tarball