PureCLIP
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skrakau
Capturing protein-RNA interaction footprints from single-nucleotide CLIP-seq data
Running Pureclip on aligned paired ended files along with aligned control paired ended files. Both have been processed in same pipeline. Getting this error: Error in function boost::math::binomial_distribution::binomial_distribution: Success fraction...
For a PureCLIP output of the form: chr1 1109065 1109066 3 3.7917 + [score_CL=3.7917;score_E=18.4394;score_B=22.2399;score_UC=3.7917] How could I filter thousands of results to focus results on more significant hits? Is there...
We are working to implement PureCLIP in our pipelines. We have some questions to address first. 1. For our purposes, need information on the peaks in order to access the...
What do I need to do to visualize the bed files generated. It looks that when I load it to IGV, and type some genes, I see no peak on...
Hi: I have tried to use pureclip to identify cross linked sites from CLIP-Seq. But when I used bam and fa from Arabidopsis, it always show errors (I have used...
Hi, I'm just wondering if pureCLIP supports multiple input BAM files? For example I have a dataset with an input control and a mock IP control. I can supply multiple...
Dear Sir: Hello, My pureclip version is 1.3.1. I meet an error like this "ERROR: Emission probability became 0.0! This might be due to artifacts or outliers. ERROR: Could not...
Hi @skrakau , I installed the package from conda. When I run the program, the process killed itself. ```shell pureclip -i aligned.prepro.R2.bam -bai aligned.prepro.R2.bam.bai \ -g ref.hg19.fa -iv 'chr1;chr2;chr3;' -nt...
Hi, the following pureclip command crashes with a coredump: pureclip -i umidedup.bam -bai umidedup.bam.bai -g homo_sapiens.88.fa -iv '1;2;3;4;8;16' -nt 8 -o PureCLIP.crosslink_sites.cov_CLmotifs.bed -nim 4 -fis fimo_clmotif_occurenc es.bed Last few output...
Hi! Sabrina I ran into this problem when running this: ``` genome=/home/hsher/genome_fa/GRCh38.p13.genome.fa motifxml=/home/hsher/pureclip_motifs/motifs.xml motiftxt=/home/hsher/pureclip_motifs/motifs.txt odir=/home/hsher/pure_output/ ip=/projects/ps-yeolab3/encode/analysis/encode_master/271_01_HNRNPC.merged.r2.bam fname=${ip##*/} prefix=${fname%.*} compute_CLmotif_scores.sh $genome $ip $motifxml $motiftxt $outdir$prefix.clmotif.bed ``` I tried`1 node and 2...
