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Merge pull request #70 from rmzelle/patch-1 

Update README.md
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Heng Li 2017-07-30 17:01:27 -04:00 committed by GitHub
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README.md
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@ -37,7 +37,7 @@ In addition to BWA, this self-consistent package also comes with bwa-associated
and 3rd-party tools for proper BAM-to-FASTQ conversion, mapping to ALT contigs,
adapter triming, duplicate marking, HLA typing and associated data files.
##Seeking helps
## Seeking help
The detailed usage is described in the man page available together with the
source code. You can use `man ./bwa.1` to view the man page in a terminal. The
@ -121,13 +121,13 @@ and only one line is primary and is soft clipped; other lines are tagged with
Yes. Since 0.6.x, all BWA algorithms work with a genome with total length over
4GB. However, individual chromosome should not be longer than 2GB.
####<a name="pe0"></a>4. Why can one read in a pair has high mapping quality but the other has zero?
#### <a name="pe0"></a>4. Why can one read in a pair have a high mapping quality but the other has zero?
This is correct. Mapping quality is assigned for individual read, not for a read
pair. It is possible that one read can be mapped unambiguously, but its mate
falls in a tandem repeat and thus its accurate position cannot be determined.
####<a name="endref"></a>5. How can a BWA-backtrack alignment stands out of the end of a chromosome?
#### <a name="endref"></a>5. How can a BWA-backtrack alignment stand out of the end of a chromosome?
Internally BWA concatenates all reference sequences into one long sequence. A
read may be mapped to the junction of two adjacent reference sequences. In this