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.
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.
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 email@example.com.
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