Similar protocols

Protocol publication

[…] The CLIP-seq reads were quality-checked by using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads mapped to rRNA, tRNA and mitochomdrial DNA sequences using Bowtie were removed from datasets. The resulting reads were mapped to the mm10 genome by using STAR with the parameters suggested in (). Piranha () was used to call peaks from the two replicates over the input control datasets with parameters ‘-b 50 s -p 0.01’. The peaks were merged using mergePeaks function in HOMER if the distance between peak centers is less than or equal to 100nt. The merged peaks were then annotated by annotatePeaks tool in HOMER to the mm10 RefSeq mRNAs. The RNA sequences of the resulting peaks were obtained using getfasta (http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html) in bedtools with parameter ‘-s’. MEME was used to search for motifs in the sequences of Clip-seq peaks with parameter ‘-w 8’. The GO term analysis of the mRNAs with Clip-seq peaks was performed by Enrichr (http://amp.pharm.mssm.edu/Enrichr/). […]

Pipeline specifications

Software tools FastQC, Bowtie, Piranha, HOMER, BEDTools, Enrichr
Application CLIP-seq analysis
Organisms Mus musculus
Diseases Infection