Unlike plant ChIP-Seq runs, most human ChIP-Seq runs had more than 60% of their reads aligning uniquely to the human reference genome. In addition, all the human control input runs had around 60% of the total reads aligning uniquely with very little variation across different runs (...
Alternatively, we can also only inputunique.sorted.bam; this will allow CLAM to call peaks using only uniquely- mapped reads. As a new feature in version 1.2.0, we implemented multi-replicate mode for peakcaller. Simply use comma to seperate bam files of replicates (Here, we assume there ...
A large number of RNA-sequencing studies set out to predict mutations, splice junctions or fusion RNAs. We propose a method, CRAC, that integrates genomic locations and local coverage to enable such predictions to be made directly from RNA-seq read analy
If desired, one can map both on the genome and on an annotated transcriptome, then use the universal scoring system of Magic-BLAST to select the best alignment, be it genomic or transcriptomic, for each fragment. In this paper, we mapped only to the genome. Output Magic-BLAST returns ...
Although protocols for NGS preparation are intended to leave little to no space for contamination of any kind, a noticeable fraction of sequencing reads still may not uniquely represent what was intended to be sequenced in the first place. If a natural consequence of a sequencing sample is to ...