{"id":22367940,"url":"https://github.com/dridk/pacbio_rna_seq","last_synced_at":"2025-03-26T16:11:31.873Z","repository":{"id":42188725,"uuid":"426579268","full_name":"dridk/pacbio_rna_seq","owner":"dridk","description":null,"archived":false,"fork":false,"pushed_at":"2022-04-11T12:49:35.000Z","size":135,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-01-31T17:52:30.776Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dridk.png","metadata":{"files":{"readme":"Readme.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-11-10T10:30:54.000Z","updated_at":"2021-11-10T13:03:43.000Z","dependencies_parsed_at":"2022-08-12T08:51:08.456Z","dependency_job_id":null,"html_url":"https://github.com/dridk/pacbio_rna_seq","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dridk%2Fpacbio_rna_seq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dridk%2Fpacbio_rna_seq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dridk%2Fpacbio_rna_seq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dridk%2Fpacbio_rna_seq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dridk","download_url":"https://codeload.github.com/dridk/pacbio_rna_seq/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245689509,"owners_count":20656417,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-12-04T18:25:16.697Z","updated_at":"2025-03-26T16:11:31.853Z","avatar_url":"https://github.com/dridk.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"This pipeline was created as part of the [GOLD project](https://aviesan.fr/fr/aviesan/accueil/menu-header/instituts-thematiques-multi-organismes/genetique-genomique-et-bioinformatique/programme-transversal-gold).\n\n\n## Installation\n#### Dependencies \n* [python \u003e= 3.9 ](https://www.python.org/downloads)\n   - seaborn\n   - pandas\n   - matplotlib\n* [seqkit](https://bioinf.shenwei.me/seqkit/)\n* [lima](https://lima.how/)\n* [fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n* [minimap2](https://lh3.github.io/minimap2/)\n* [samtools](http://www.htslib.org/)\n* [bedtools](https://bedtools.readthedocs.io/en/latest/) \n\n#### Install environment from conda \n\n```bash\nconda env create -n gold -f env.yaml\n````\n\n## Usage \n\n#### Clone the repository\n\n```bash\ngit clone git@github.com:dridk/pacbio_rna_seq.git\n```\n\n#### Edit config.yaml\n- ```FASTQ``` The Fastq file path generated by PacBio Sequencing \n- ```BARCODE``` The Fasta file path describing barcodes used by lima for demultiplexing ( see example in repository ) \n- ```PRIMERS``` The Fasta file describing primers used for PacBio amplicon sequencing ( see example in repository ) \n- ```REFERENCE``` The fasta reference file used by minimap2 for alignement ( e.g: hg19.fa ) \n\n\n#### Run the pipeline \n\nPut ```your_file.fastq``` generated by PacBio in the same folder than *config.yaml* and run the following command. \nYou can edit how many threads you want to use with ```--cores``` option.\n\n```\nsnakemake -Fp --cores 10 --configfile config.yaml \n```\n\n## Output \n\nThe pipeline will generate one file per barcode and amplicon. \nFor instance HBB.bc1022.bam contains aligned reads from HBB amplicon and bc1022 barcode identifer.\n\n- ```debarcoding.{barcode}--{barcode}.fastq``` : Demultiplexed reads \n- ```{amplicon}.{barcode}.fastq```  : Transcripts reads\n- ```{amplicon}.{barcode}.bam```  : Aligned transcripts Reads \n- ```{amplicon}.{barcode}.bed```  : Transcripts structures as a bed file \n- ```{amplicon}.{barcode}.hash.bed```  : Transcripts structures as a bed file with a unique ID to identify the transcript\n- ```{amplicon}.{barcode}.hash.png```  : Distribution plot of transcripts\n- ```cluster.{amplicon}.png```  : Transcripts abundance heatmap \n\nFor instance, the following heatmap shows transcript abundances for each barcode. \nEach transcript is identified by a hash number generated from the transcript structure bed file. \nThis make possible to identify transcripts among differents samples.\n\n![](https://github.com/dridk/pacbio_rna_seq/blob/5eadf2b089f1a6839397985baf873084898598b3/cluster.ACKR1.png)\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdridk%2Fpacbio_rna_seq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdridk%2Fpacbio_rna_seq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdridk%2Fpacbio_rna_seq/lists"}