Description
This track was created by mapping D. mojavensis RNA-Seq reads from head tissues
against the D. mojavensis DmojImproved genome assembly using TopHat2. The RNA-Seq data
were generated by modENCODE project and the raw data is available for download at
the NCBI Sequence Read Archive (SRA):
| Accession number | Description | Platform |
|---|
| SRX017458 |
Female heads (rep1) |
Illumina Genome Analyzer |
| SRX017459 |
Female heads (rep2) |
Illumina Genome Analyzer II |
| SRX017460 |
Male heads (rep1) |
Illumina Genome Analyzer |
| SRX017461 |
Male heads (rep2) |
Illumina Genome Analyzer II |
The TopHat junction predictions from the different libraries are filtered
and merged together into a single set of predictions. The predictions are
color-coded based on the number of reads supporting the junction:
| Color | Number of reads |
|---|
| > 1000 |
| 500-999 |
| 100-499 |
| 50-99 |
| 10-49 |
| < 10 |
Methods
TopHat2 was run against the D. mojavensis genome using the following
parameters: -g 1 --b2-very-sensitive --min-intron-length 30 --max-intron-length 150000
References
TopHat is
a fast splice junction mapper for RNA-Seq reads.
It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner
Bowtie, and then analyzes the mapping results to identify
splice junctions between exons.
The RNA-Seq data were submitted by the modENCODE project.
The original RNA-Seq dataset can be obtained from the NCBI GEO database under the accession number
GSE20882.
|