Description

This track displays depth of coverage from CB4856 mixed-stage RNAseq reads generated by the Rajewsky lab at the Max Delbruck Center for Molecular Medicine. Splice junction mapping to the reference was completed using TopHat (described below).

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 100x by default; this (and other) parameters can be adjusted as desired in the Track Settings.

Methods

Three polyA-selected mixed-stage CB4856 RNAseq datasets, recently generated by Stoeckius et al, were downloaded. 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 from the Short Read Archive as experiments SRX533802, SRX533803, and SRX533804.

Thanks to the Rajewsky lab for their CB4856 RNAseq dataset, to Daehwan Kim, Steven Salzberg, and Cole Trapnell for their work creating TopHat, and to Heng Li for his work creating samtools.

References

Stoeckius M, Grün D, Rajewsky N. Paternal RNA contributions in the Caenorhabditis elegans zygote. EMBO J. 2014;33(16):1740-50. PMID 24894551

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.