Similar protocols

Protocol publication

[…] To quantify average transcript levels on X and autosomes we used RNA-seq data generated in () and similar protocols for analysis. Libraries were sequenced with Illumina’s HiSeq 2000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further. To remove and trim reads containing the sequencing barcodes, we used cutadapt version 0.9.5 (https://cutadapt.readthedocs.org/) (). Reads were aligned to the WS220 transcriptome using GSNAP version 2012-01-11 (). Uniquely mapping reads were assigned to genes using HTSeq version 0.5.4p3 using the union mode (). We used DESeq to calculate normalization factors and for significance testing (). To calculate expression level of individual genes, the normalized expression values from DESeq were divided by gene length (kb). Gene expression boxplots were generated using either all genes with a normalized expression level greater than zero or genes within the top 90% of expressed genes.Raw reads from RNA-seq experiments in L4 animals with and without germlines were downloaded from the NIH short read archive (). For the N2 transcriptome, we used the files SRR023579.sra, SRR023580.sra, and SRR023581.sra. For the glp-1(q224) germlineless transcriptomes, we used the files SRR031122.sra and SRR031123.sra. Reads were processed using the approach above. […]

Pipeline specifications

Software tools BaseSpace, cutadapt, GSNAP, HTSeq, DESeq
Application RNA-seq analysis
Organisms Caenorhabditis elegans