Description
This track was created by mapping D. mojavensis RNA-Seq reads 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 |
|---|
| SRX054488 | SRR166836 |
Adult females (rep1) |
Illumina Genome Analyzer II |
| SRX054489 | SRR166837 |
Adult females (rep2) |
Illumina HiSeq 2000 |
| SRX247002 | SRR768439 |
Adult males (rep1) |
Illumina Genome Analyzer II |
| SRX247003 | SRR768440 |
Adult males (rep2) |
Illumina HiSeq 2000 |
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: --no-mixed --no-discordant -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
GSE28078.
|