198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html index 5c44a931290..fe96219d3df 100644 --- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html +++ src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html @@ -6,31 +6,31 @@ which was done here on an Illumina Genome Analyzer (GAI or GAIIx) (Mortazavi et al., 2008). The transcriptome measurements shown on these tracks were performed on polyA selected RNA from total cellular RNA using two different protocols - one that preserves information about which strand the read is coming from and one that does not. Due to the specifics of the enzymology of library construction, gene and transcript quantification is more accurate based on the non-strand-specific protocol, while the strand-specific protocol is useful for assigning strandedness, but in general less reliable for quantification.

Non-strand-specific protocol (deep "reference" transcriptome measurements, 2x75 bp reads):

PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis and then converted into cDNA by random priming and amplified. Data have been produced in two formats: single reads, each of which comes from one end of a cDNA molecule, and paired-end reads, which are obtained as pairs from both ends of cDNAs. This RNA-seq protocol does not specify the coding strand. As a result, there will be ambiguity at loci where both strands are transcribed. The "randomly primed" reverse transcription is, apparently, not fully random. This is inferred from a sequence bias in the first residues of the read population, and this likely contributes to observed unevenness in sequence coverage across transcripts.

Strand specific protocol (1x75 bp reads):

-

PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis. 3′ adapters were ligated to the 3′ end of fragments, then 5′ adapters were ligated to the the 5′ end. +

PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis. 3′ adapters were ligated to the 3′ end of fragments, then 5′ adapters were ligated to the 5′ end. The resulting RNA molecules were converted to cDNA and amplified. This RNA-seq protocol does specify the coding strand as each read is in the same 5′-3′ orientation as the original RNA strand. As a result, loci where both strands are transcribed can be disambiguated. However, RNA ligation is an inherently biased process and as a result greater unevenness in sequence coverage across transcripts is observed compared to the non-strand-specific data, and quantification is less accurate.

Data Analysis:

Reads were aligned to the hg19 human reference genome using TopHat, a program specifically designed to align RNA-seq reads and discover splice junctions de novo. Cufflinks, a de novo transcript assembly and quantification software package, was run on the TopHat alignments to discover and quantifiy novel transcripts and to obtain trascript expression estimates based on the GENCODE annotation. All sequence files, alignments, gene and transcript models and expression estimates files are available for download

Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view