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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, and 3rd-party tools for proper BAM-to-FASTQ conversion, mapping to ALT contigs,
adapter triming, duplicate marking, HLA typing and associated data files. 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 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 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 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. 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 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 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. 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 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 read may be mapped to the junction of two adjacent reference sequences. In this