updated README.md

Author: rishvanth-kp

README.md

@@ -29,17 +29,22 @@ The mapped fragments are given to a script that filters ambiguously
 mapped fragments:
 ```
 ./filterAlnScoreAndQual.py -i mapped_smurf_reads.sam \
-  -o unambig_smurf_frags.sam -s 120 -q 1
+    -o unambig_smurf_frags.sam -s 120 -q 1
 ```
 
+The input file `mapped_smurf_reads.sam` is just the mapped reads
+(e.g. with BWA). The output file `unambig_smurf_frags.sam`
+contains mapped fragments with mapping quality greater than or equal
+to 1.
+
 Then the remaining fragments are given to a script that obtains
 the counts of reads in bins:
 ```
 ./getBinCounts.py -i unambig_smurf_frags.sam -c hg19.chrom.sizes \
     -b bins_5k_hg19.bed -o bin_counts.bed -s bin_stats.txt
 ```
-The input file `mapped_smurf_reads.sam` is just the mapped reads
-(e.g. with BWA). The file `hg19.chrom.size` is the size of all chroms
+The input file `unambig_smurf_frags.sam` is the same as described above. 
+The file `hg19.chrom.size` is the size of all chroms
 in the reference genome. This file for the hg19 reference is supplied
 in the `data` directory in this repo, and was obtained from the UCSC
 Genome Browser's database. The pre-defined bins file `bins_5k_hg19.bed`
@@ -164,7 +169,7 @@ well it recovers the known mapping locations. The steps are as follows.
     `bedtools` (we used v2.26.0). We also require the `deadzones`
     program from `http://github.com/smithlabcode/utils` but this could
     be substituted for any means of excluding unmappable regions.
-    In our CNV analysis, we used `bwa` (version...).
+    In our CNV analysis, we used `bwa` (0.7.17).
 
 ## Contacts and Bug Reports
 

test/README.md

@@ -1,10 +1,6 @@
-## To test mapping a simulated SMURF-seq read to a
-## small simulated genome
-../map/smurfseq-map.sh map/ref_sim.fa map/read_sim.fastq
+## To test mapping simulated SMURF-seq reads to a small simulated genome
+A simulated reference genome `ref_sim.fa` has been indexed with BWA-MEM.
+`read_sim.fastq` contains simulated reads.
 
-## Generate CNV profile
-../cnv/cnv-5k.sh map/read_sim.fastq.2x.sam test_cnv
-
-## To test mapping a simulated-read to the human
-## genome
-../map/smurfseq-map.sh [path to human genome] map/read_hg.fastq
+## To test mapping simulated reads to the human genome
+`read_hg.fastq` contains simulated reads from the human genome.