Features for bigChain and bigPsl and a new setting: otherTwoBitUrl

[Brian Lee]

There's new documentation on the Track Hub Database Definitions page (http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html) for adding coloring options to chains and psl in Track Hubs with the bigChain and bigPsl formats and a new otherTwoBitUrl setting to support alignment tracks. Read more about bigChain (http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#bigChain_-_Pairwise_Alignments) or about bigPsl (http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments) tracks.

otherTwoBitUrl

http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#otherTwoBitUrl

For pairwise alignment tracks this can specify where to find the query sequence. This setting can be used in psl, bigPsl, chain, and bigChain tracks.

--- coloring options --

baseColorUseSequence 

http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#baseColorUseSequence

Specifies where item sequence can be found (if any) so that item sequence, or differences from genomic sequence, can be drawn when viewing a sufficiently small region.

baseColorDefault

http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#baseColorDefault

Specifies the default drawing mode. The itemBases, itemCodons, diffBases and diffCodons options are applicable only if the track has sequence, as specified by the baseColorUseSequence setting. The genomicCodons, itemCodons and diffCodons are applicable only if the track has CDS info, as specified by the baseColorUseCds setting.

baseColorDefault

http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#baseColorDefault

Insertion and deletion differences between tag sequences and the reference genome can be highlighted with the use of these settings. These options may be set by the user.

• indelDoubleInsert: Use to highlight alignment gaps in both the target (reference) and query (tag) sequence with double (=) lines.
• indelQueryInsert: Use to highlight an insert in the query sequence only by drawing an orange (|) or purple (|) vertical line. Orange lines show unalignable regions in the middle of a sequence, and purple highlights regions at the end of the query sequence.
• indelPolyA: Use to highlight an apparently valid poly-a tail by drawing a vertical green line (|).

[Brian Lee]

Correction: The last item was indelDoubleInsert,  read more in bigChain (http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#bigChain_-_Pairwise_Alignments) or bigPsl (http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments) sections.

indelDoubleInsert

Insertion and deletion differences between tag sequences and the reference genome can be highlighted with the use of these settings. These options may be set by the user.

• indelDoubleInsert: Use to highlight alignment gaps in both the target (reference) and query (tag) sequence with double (=) lines.
• indelQueryInsert: Use to highlight an insert in the query sequence only by drawing an orange (|) or purple (|) vertical line. Orange lines show unalignable regions in the middle of a sequence, and purple highlights regions at the end of the query sequence.
• indelPolyA: Use to highlight an apparently valid poly-a tail by drawing a vertical green line (|).