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Welcome to the clipper wiki!

CLIPper is a tool to define peaks in your CLIP-seq dataset.

Installing CLIPper is (should be) easy! Using git, you can clone the most recent version of this repository to a writable location on your system.

Before you use CLIPper, you'll have to generate mapped reads. This can be accomplished many ways, but we recommend using an aligner which is tolerant of spliced reads, in the future we will include options to detect mRNA-bound vs pre-mRNA-bound transcripts. We prefer to use GSNAP for this, but you may use other algorithms; however, note that all testing is done with GSNAP-derived mapped reads.

An example mapping procedure using gsnap could be this:

initial pre-processing: raw_reads ---> <Quality control> ---> <Trim sequencing adaptor sequences> ---> CLIP-seq_reads.gz

gsnap -t 4 -N 1 -A sam --gunzip -B 5 -s mm9 -d mm9 CLIP-seq_reads.gz > CLIP-seq_reads.sam
samtools view -bS CLIP-seq_reads.sam > CLIP-seq_reads.bam
samtools sort CLIP-seq_reads.bam CLIP-seq_reads.srt
samtools flagstat CLIP-seq_reads.srt.bam > CLIP-seq_reads.mapStats.txt

if you decide you want to remove reads with redundant start/stop positions (If you're not sure, then omit this step. You can ask CLIPper to collpase these later).

samtools rmdup -s CLIP-seq_reads.srt.bam CLIP-seq_reads.srt.rmdup.bam
samtools flagstat CLIP-seq_reads.srt.rmdup.bam >> CLIP-seq_reads.mapStats.txt

Then index your bam alignment:

samtools index CLIP-seq_reads.srt.bam