CAGE from Khamis et al., 2015 (hub_24769_AllCagePlus)
  Position: chrLG5:7,649,858-7,653,858
Total Bases in view: 4,001
Statistics on: 1 items covering 1 bases (0.02% coverage)
Average item spans 1.00 bases.
Average value 3 min 3 max 3 standard deviation 0
View table schema

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Description

This track represents the 5′ end of CAGE reads generated by Khamis et al. (2015) and is based on the samples GSM1568470 and GSM1568471. Note than only the 5′-end coordinate of each read was retained, facilitating the visual identification of the putative TSS. An overview of all the tracks provided by EPD for the amel5 assembly can be seen in table format here.

Methods

Raw data in SRA format was downloaded from GEO. FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0). Following the manuscript's protocol, paired-end reads were split according to 8 different barcodes into the biological replicates. Subsequently, reads were trimmed of the 21 bp-long adapter at the 5′ end and mapped to the genome using Bowtie2 v2.2.9. SAM files were then converted into BAM using samtools v0.1.14 and to BED using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2). All replicates were merged, and the WIG file was generated with a step parameter set to 1.

Credits

Data were generated by Khamis et al. (2015) and processed by the EPD team at the Swiss Institute of Bioinformatics (Dreos et al. 2013). For inquiries, please contact us using the online form here or post a message on ask-epd@googlegroups.com.

References

Khamis AM, Hamilton AR, Medvedeva YA, Alam T, Alam I, Essack M, Umylny B, Jankovic BR, Naeger NL, Suzuki M, Harbers M, Robinson GE, Bajic VB. Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. Sci Rep. 2015 Jun 15;5:11136. doi: 10.1038/srep11136. PMID: 26073445

Dreos R, Ambrosini G, Perier RC, Bucher P. EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res. 2013 Jan 1;41(D1):D157-64. PMID: 23193273