ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-12-16T16:21:28+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/164[Hi-C] Hi-C pipeline developpement2022-12-16T16:21:28+01:00Claire Kuchly[Hi-C] Hi-C pipeline developpementImplementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer re...Implementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer result (file inter.txt) interface with smartyClaire KuchlyClaire Kuchly2020-04-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/149[Sequel2] make new qc pipeline for Sequel2 data2022-12-16T16:21:28+01:00Claire Kuchly[Sequel2] make new qc pipeline for Sequel2 dataRaw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CL...Raw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CLR data : all files in output directory
Create of one analysis of run_stat.
? Make available fastq file.
?Claire KuchlyClaire Kuchly2020-01-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/142manage run 10X with samples with custom index that have to be processed like ...2022-12-16T16:21:27+01:00Claire Kuchlymanage run 10X with samples with custom index that have to be processed like 10X samplesLike SOCSMURIS projects : [mantis 4657](https://genomique.genotoul.fr/Mantis/view.php?id=4657), 10X samples and other samples in the same lane with longranger demultiplexing.
Rigth now, only sample with 10X indexes can be analyse with 1...Like SOCSMURIS projects : [mantis 4657](https://genomique.genotoul.fr/Mantis/view.php?id=4657), 10X samples and other samples in the same lane with longranger demultiplexing.
Rigth now, only sample with 10X indexes can be analyse with 10X illumina qc workflow.Claire KuchlyClaire Kuchly