* Merge from branches/dev/

[samtools.git] / examples / 00README.txt

diff --git a/examples/00README.txt b/examples/00README.txt
index 5dd123cb1eaa65b4c88815f1fe0366ed75bbbaa7..dbb276f467124d3eab407a22657949be27000c4d 100644 (file)
--- a/examples/00README.txt
+++ b/examples/00README.txt
@@ -1,28 +1,23 @@
-NA18507_part.fa contains two sequences cut from the human genome
+File ex1.fa contains two sequences cut from the human genome
 build36. They were exatracted with command:
 
   samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550
 
-Sequence names were changed manually for simplicity. ex1.fa.fai is the
-index for the sequence file, generated by:
-
-  samtools faidx ex1.fa
-
-This index file also works as the reference list file used by `import'
-and `pileup' commands of samtools. ex1.sam.gz contains MAQ alignments
-exatracted with:
+Sequence names were changed manually for simplicity. File ex1.sam.gz
+contains MAQ alignments exatracted with:
 
   (samtools view NA18507_maq.bam 2:2044001-2045500;
    samtools view NA18507_maq.bam 20:68001-69500)
 
-and processed with an awk command to make everything consistent as a
+and processed with `samtools fixmate' to make it self-consistent as a
 standalone alignment.
 
 To try samtools, you may run the following commands:
 
-  samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-  samtools index ex1.bam
-  samtools tview ex1.bam ex1.fa
-  samtools pileup -cf ex1.fa ex1.bam
+  samtools faidx ex1.fa                 # index the reference FASTA
+  samtools import ex1.fa.fai ex1.sam.gz ex1.bam   # SAM->BAM
+  samtools index ex1.bam                # index BAM
+  samtools tview ex1.bam ex1.fa         # view alignment
+  samtools pileup -cf ex1.fa ex1.bam    # pileup and consensus
   samtools pileup -cf ex1.fa -t ex1.fa.fai ex1.sam.gz