juicer

juicer copied to clipboard

Use bwa-mem2 mem to accelerate the pipeline

1

Hi dear developers, Thanks for your great work! I noticed the bwa mem had an updated version [bwa-mem2 mem](https://github.com/bwa-mem2/bwa-mem2) which rapidly accelerate the mapping step to half the time before...

tinyfallen

java error while running juicer on cluster

2

Dear Juicer team, I am running HiC data using CPU version on our server system at Ugent. Can you tell me am i doing anything wrong here or is it...

BijalThakkar

How to input the eigenvertor result into the juicebox to visualization.

3

When i use the juicer eigenvector to get a result file. But i can not put the result into the juicebox. What should i do to switch the result file...

phil622

Thank you very much! The juicer software is very powerful and useful.I got the .HiC data using juicer software default resolution(Maximum resolution is only 5kb ) and merged the biological...

shenlinyong

problem with Running on already aligned files

2

The -S chimeric option is not available anymore with the latest version of juicer. When I tried to use the -S merge to run on already aligned HiC bam file...

mycecilia

Take long time to generate .hic file

1

Hello, I run juicer on a 5G bp genome to place contigs using HiC data, but it take weeks to generate the interaction matrix (.hic file). It seems there is...

starnight0

Chromosome combination error in mega.sh

2

Hi, I am encountering an error when running mega.sh to combine contacts from different biological replicates using mega.sh. ``` Using 1 CPU thread(s) for primary task Using 10 CPU thread(s)...

kellyliyichen

[-d topDir] argument is not passed correctly to -i argument for postprocessing

1

**Describe the bug** When running the juicer pipeline with the following command `./opt/scripts/juicer.sh -S final -D $(readlink -f opt) -z $(pwd)/opt/references/hg38.p13.fa.gz -d $(pwd)/L79851_Track-123454/ -p hg38 -t 32` it is not...

Norbittner

merge: invalid option -- 'c'

2

This problem (-: Aligning files matching /home/xuxiao/biosoftware/genemoe/asemmbly/juicer/work/test/fastq/*_R*.fastq* to genome /home/xuxiao/biosoftware/genemoe/asemmbly/juicer/references/test/contigs.fa with no fragment delimited maps. merge: invalid option -- 'c' merge: invalid option -- 't' open: No such file or...

worldxiao

statistics of hic contacts in inter.txt looks abnormal

1

**Are you sure this is an issue?** Github Issues is reserved for situations that require changes to the codebase. Questions, discussions, etc. should be posted to the forum: aidenlab.org/forum.html Dear...

JiaoLaboratory