Description

Two supplemental RNAseq datasets are provided with the CB4856 reference browser. This track, CB_L4_RNAseq, consists of 4,757,347 paired-end 51bp reads from CB4856 worms at developmental stage L4. The other track, N2_L4_RNAseq, is an identically prepared N2 sample providing 9,291,076 paired-end 51bp reads. Much deeper and less stage-specific CB4856 RNAseq datasets are available (i.e. the Mixed Stage RNA track available from the Rajewsky lab), but this one is provided here because it was generated with an N2 control.

Display Conventions and Configuration

Coverage depth is displayed in WIG format. Many transcripts are deeply covered, so the maximum vertical viewing range is set to 75x by default; this (and other) parameters can be adjusted as desired in the Track Settings.

Methods

The L4 CB4856 RNAseq dataset was obtained from Basten Snoek and Jan Kammenga, and reads were aligned to the CB4856 reference genome with TopHat 2.0.6 (calling bowtie2 2.0.0-beta6) using the command "--b2-fast". The resultant bam files were sorted and merged, and coverage data was extracted using the samtools (version 0.1.18) mpileup command.

Credits

Please feel free to contact Owen Thompson with any questions and/or concerns regarding this or other tracks.

The raw data used to generate the depth of coverage displayed here is available upon request from either the Kammenga lab or the Waterston lab. It has not been deposited to the SRA as it was not used to contribute substantially to the generation (or annotation) of the CB4856 reference sequence; we provide this track simply to supplement any transcript studies in CB4856 requiring a careful N2 control.

Thanks to Basten Snoek and Jan Kammenga for generating this dataset.

References

Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105-11. PMID 19289445.

Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9. PMID 19505943.