How to run HiCUP

[@oksana03fel]

Hi. I tried to run a pipeline followed by this video. But at the end i don't have a summary report file. Who can help me to find the solution? Thank you.

[@BabrahamBioinf]

Steven Wingett no longer works for Babraham Bioinformatics, please visit:github.com/StevenWingett/HiCUP/issues and click the “New Issue” button.

[@mei-yuqiu6471]

hi, when I try to run "hicup_v0.6.1/hicup --config hicup_example.conf" same as shown in the video, I got an error "Can't exec "/home/users/myqiu/bin/Rscript": No such file or directory at /home/us ers/myqiu/Project/HiCCUP/hicup_v0.6.1/hicup_truncater line 443." and "Could not produce hicup_truncater summary bar chart: /home/users/myqiu/bin/Rscrip t /home/users/myqiu/Project/HiCCUP/hicup_v0.6.1/r_scripts/hicup_truncater_summary .r ./ ./hicup_truncater_summary_18-33-31_28-06-2018.txt: No such file or director y at /home/users/myqiu/Project/HiCCUP/hicup_v0.6.1/hicup_truncater line 443.". its quite confusing.

[@BabrahamBioinf]

Have a look where you set your R location, either in your config file or on the command line. You are asked to provide the path to R, but the actual binary which is run is the Rscript binary which should be in the same directory. Either your setting for the location of R is incorrect (~/bin/) or you need to add in a link to the Rscript binary in your R install to the same location.

[@BabrahamBioinf]

If you have further problems, please feel free to email me on [e-mail]

[@BabrahamBioinf]

Steven Wingett no longer works for Babraham Bioinformatics, please visit:github.com/StevenWingett/HiCUP/issues and click the “New Issue” button.

[@VinodSinghatjnu]

hi please tell me from where you took Genome_Aligner_Indices folder

[@simonandrews5604]

HiCUP uses the bowtie2 aligner so you'll need to have downloaded the fasta files for the genome you're using and have indexed them with the bowtie2-build program which comes with bowtie2. There is a quick summary of how to do this in the written HiCUP guide at www.bioinformatics.babraham.ac.uk/projects/hicup/quickstart/ - it's pretty simple to do but takes a while on large genomes.

[@yoyemaye9680]

Hi, I didn´t understood the difference between Unique Alignments and Paired, could you teel me please? :)

[@simonandrews5604]

Unique and paired aren't really related. Unique alignments are simply alignments where there was only one place in the genome where there was a convincing sequence match. For some repetitive sequences there may be many places in the genome with virtually identical sequence so you can't be confident that you're choosing the right one, so we only deal with Unique alignments where this isn't an issue. Paired alignments are where you have two sequences (a pair) to align. In HiCUP terms this would be the sequences from either end of the di-tag which provide the linkage between different genomic regions. Unique pairs would be paired sequences where both of the sequences were uniquely aligned.

[@plastoquinoneplastoquinone6939]

Hi, there is a problem when I run the test data,after pairing complete, it showed that "Can't read './test_dataset1.map.sam' : No such file or directory at /Share/home/shenxh/LAB_DATA/PQ/HiCUP/hicup_v0.5.9/hicup_mapper line 573.", would you please help me to solve this? Thanks.

[@BabrahamBioinf]

Hi, Please send [e-mail] the HiCUP output written to your screen (standard out). We will try and diagnose what has happened.