I never used Tophat v1.1.1 which listed a fix for the sam sort header (see below) but in newest version, TopHat v1.2.0 all my sam files have sort headers of "sorted" not "coordinate". Oddly, parsing the file through Samtools sort does not fix the problem but parsing it through Picard does. Also the sam headers are not listed in numeric order:
Such as:
chr1
chr11
chr12
...
chr2
chr20
Not:
chr1
chr2
chr3
chr4
Anyone else seeing these minor issues?
----Previous release notes-----
TopHat 1.1.1 release 10/11/2010
This release of TopHat includes some fixes related to Colorspace read mapping.
* Negative quality values are now handled correctly.
* Comments at the beginning of csfasta files no longer trigger an error.
* --integer-quals no longer conflicts with -i
* The header in TopHat BAM files now correctly lists the sort order as coordinate, with group order reference
Such as:
chr1
chr11
chr12
...
chr2
chr20
Not:
chr1
chr2
chr3
chr4
Anyone else seeing these minor issues?
----Previous release notes-----
TopHat 1.1.1 release 10/11/2010
This release of TopHat includes some fixes related to Colorspace read mapping.
* Negative quality values are now handled correctly.
* Comments at the beginning of csfasta files no longer trigger an error.
* --integer-quals no longer conflicts with -i
* The header in TopHat BAM files now correctly lists the sort order as coordinate, with group order reference
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