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| { | ||
| "full-splice_match": [ | ||
| { | ||
| "perc_A_downstream_TTS":[0,59] | ||
| } | ||
| ], | ||
| "rest": [ | ||
| { | ||
| "perc_A_downstream_TTS":[0,59], | ||
| "all_canonical":"canonical", | ||
| "RTS_stage":"FALSE" | ||
| }, | ||
| { | ||
| "perc_A_downstream_TTS":[0,59], | ||
| "RTS_stage":"FALSE", | ||
| "min_cov":0 | ||
| } | ||
| ] | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,25 @@ | ||
| Sample Sample Number of Iso-Seq Reads Number of ONT Reads Genotype Age (months) | ||
| K19 Mouse 1 49638 - WT 4 | ||
| K23 Mouse 2 51020 - WT 8 | ||
| K21 Mouse 3 53727 - WT 6 | ||
| K18 Mouse 4 63328 - TG 2 | ||
| K20 Mouse 5 59153 - TG 4 | ||
| K17 Mouse 6 50058 - WT 2 | ||
| S19 Mouse 7 24293 738056 WT 4 | ||
| K24 Mouse 8 25705 763528 TG 8 | ||
| L22 Mouse 9 28081 807960 TG 8 | ||
| M21 Mouse 10 27351 725260 WT 2 | ||
| O18 Mouse 11 27135 824401 TG 2 | ||
| O23 Mouse 12 24598 800543 WT 8 | ||
| O22 Mouse 13 25283 765738 TG 6 | ||
| P19 Mouse 14 22427 730010 WT 6 | ||
| T20 Mouse 15 26239 819564 TG 6 | ||
| Q20 Mouse 16 28114 1317511 TG 8 | ||
| Q21 Mouse 17 23770 1080464 WT 2 | ||
| S18 Mouse 18 27546 1131981 TG 2 | ||
| S23 Mouse 19 24322 998458 WT 8 | ||
| Q18 Mouse 20 32683 1295303 TG 6 | ||
| Q17 Mouse 21 13861 666928 WT 6 | ||
| L18 Mouse 22 16530 793802 TG 4 | ||
| Q23 Mouse 23 18572 1117300 WT 4 | ||
| T18 Mouse 24 24938 1150108 TG 4 |
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| Original file line number | Diff line number | Diff line change |
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| Sample Sample Number of Reads Genotype Age (months) | ||
| K23 Mouse 2 351454 WT 8 | ||
| K18 Mouse 4 338557 TG 2 | ||
| K17 Mouse 6 329636 WT 2 | ||
| K24 Mouse 8 350120 TG 8 | ||
| L22 Mouse 9 328831 TG 8 | ||
| M21 Mouse 10 339563 WT 2 | ||
| O18 Mouse 11 212387 TG 2 | ||
| O23 Mouse 12 329376 WT 8 | ||
| Q20 Mouse 16 342173 TG 8 | ||
| Q21 Mouse 17 227113 WT 2 | ||
| S18 Mouse 18 358413 TG 2 | ||
| S23 Mouse 19 354154 WT 8 |
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| Original file line number | Diff line number | Diff line change |
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| >primer_5p | ||
| AAGCAGTGGTATCAACGCAGAGTACATGGG | ||
| >primer_3p | ||
| GTACTCTGCGTTGATACCACTGCTT |
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50 changes: 50 additions & 0 deletions
50
A_Global_Transcriptome/1_IsoSeq_Pipeline/1b_J20_run_isoseq3.sh
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| #!/bin/bash | ||
| #SBATCH --export=ALL # export all environment variables to the batch job | ||
| #SBATCH -D . # set working directory to . | ||
| #SBATCH -p mrcq # submit to the parallel queue | ||
| #SBATCH --time=20:00:00 # maximum walltime for the job | ||
| #SBATCH -A Research_Project-MRC148213 # research project to submit under | ||
| #SBATCH --nodes=1 # specify number of nodes | ||
| #SBATCH --ntasks-per-node=16 # specify number of processors per node | ||
| #SBATCH --mail-type=END # send email at job completion | ||
| #SBATCH [email protected] # email address | ||
| #SBATCH --array=0-1 # 2 samples | ||
| #SBATCH --output=1b_J20_run_isoseq3-%A_%a.o | ||
| #SBATCH --error=1b_J20_run_isoseq3-%A_%a.e | ||
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| # J20 samples | ||
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| ##------------------------------------------------------------------------- | ||
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| # source config file and function script | ||
| module load Miniconda2/4.3.21 | ||
| SC_ROOT=/lustre/projects/Research_Project-MRC148213/sl693/scripts/rTg4510/A_Global_Transcriptome | ||
| source $SC_ROOT/1_IsoSeq_Pipeline/rTg4510_isoseq.config | ||
| source $SC_ROOT/1_IsoSeq_Pipeline/01_source_functions.sh | ||
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| ##------------------------------------------------------------------------- | ||
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| # run as array (defined in config file) | ||
| rawDir=/lustre/projects/Research_Project-MRC148213/sl693/rTg4510/1_raw/A_WholeTranscriptome/J20_PacBio | ||
| SAMPLE=${J20_ALL_SAMPLE_NAMES[${SLURM_ARRAY_TASK_ID}]} | ||
| J20_BAM_FILES=($rawDir/m54082_190302_104610.subreads.bam $rawDir/m54082_180816_074627.subreads.bam) | ||
| BAM_FILE=${J20_BAM_FILES[${SLURM_ARRAY_TASK_ID}]} | ||
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| ##------------------------------------------------------------------------- | ||
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| # Isoseq3.4.0 | ||
| # run_CCS_batch <input_ccs_bam> <prefix_output_name> <Output_directory> | ||
| # run_LIMA $Sample $Input_CCS_directory $Output_directory <"no_multiplex"/"multiplex"> | ||
| # run_REFINE $Sample $Input_LIMA_directory $Output_directory | ||
| # run_CLUSTER $Sample $Input_REFINE_directory $Output_directory | ||
| run_CCS ${BAM_FILE} ${SAMPLE} ${WKD_ROOT}/1_isoseq3/1_ccs | ||
| run_LIMA ${SAMPLE} ${WKD_ROOT}/1_isoseq3/1_ccs ${WKD_ROOT}/1_isoseq3/2_lima "no_multiplex" | ||
| run_REFINE ${SAMPLE} ${WKD_ROOT}/1_isoseq3/2_lima ${WKD_ROOT}/1_isoseq3/3_refine | ||
| run_CLUSTER ${SAMPLE} ${WKD_ROOT}/1_isoseq3/3_refine ${WKD_ROOT}/1_isoseq3/4_cluster | ||
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| ##------------------------------------------------------------------------- | ||
| #run_star ${SAMPLE} ${RNASEQ_FILTERED_DIR} ${RNASEQ_MAPPED_DIR} |
52 changes: 52 additions & 0 deletions
52
A_Global_Transcriptome/1_IsoSeq_Pipeline/1c_J20_run_isoseq3.sh
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| #!/bin/bash | ||
| #SBATCH --export=ALL # export all environment variables to the batch job | ||
| #SBATCH -D . # set working directory to . | ||
| #SBATCH -p mrcq # submit to the parallel queue | ||
| #SBATCH --time=20:00:00 # maximum walltime for the job | ||
| #SBATCH -A Research_Project-MRC148213 # research project to submit under | ||
| #SBATCH --nodes=1 # specify number of nodes | ||
| #SBATCH --ntasks-per-node=16 # specify number of processors per node | ||
| #SBATCH --mail-type=END # send email at job completion | ||
| #SBATCH [email protected] # email address | ||
| #SBATCH --array=0-1 # 2 samples | ||
| #SBATCH --output=1c_J20_run_isoseq3-%A_%a.o | ||
| #SBATCH --error=1c_J20_run_isoseq3-%A_%a.e | ||
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| # J20 samples: E18 and B21 | ||
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| ##------------------------------------------------------------------------- | ||
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| # source config file and function script | ||
| module load Miniconda2/4.3.21 | ||
| SC_ROOT=/lustre/projects/Research_Project-MRC148213/lsl693/scripts/rTg4510/A_Global_Transcriptome | ||
| source $SC_ROOT/1_IsoSeq_Pipeline/rTg4510_isoseq.config | ||
| source $SC_ROOT/1_IsoSeq_Pipeline/01_source_functions.sh | ||
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| ##------------------------------------------------------------------------- | ||
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| # run as array (defined in config file) | ||
| rawDir=/lustre/projects/Research_Project-MRC148213/lsl693/rTg4510/1_raw/A_WholeTranscriptome/J20_PacBio | ||
| J20_ALL_SAMPLE_NAMES=(E18 B21) | ||
| J20_BAM_FILES=($rawDir/m54082_180818_105629.subreads.bam $rawDir/m54082_190303_070925.subreads.bam) | ||
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| SAMPLE=${J20_ALL_SAMPLE_NAMES[${SLURM_ARRAY_TASK_ID}]} | ||
| BAM_FILE=${J20_BAM_FILES[${SLURM_ARRAY_TASK_ID}]} | ||
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| ##------------------------------------------------------------------------- | ||
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| # Isoseq3.4.0 | ||
| # run_CCS_batch <input_ccs_bam> <prefix_output_name> <Output_directory> | ||
| # run_LIMA $Sample $Input_CCS_directory $Output_directory <"no_multiplex"/"multiplex"> | ||
| # run_REFINE $Sample $Input_LIMA_directory $Output_directory | ||
| # run_CLUSTER $Sample $Input_REFINE_directory $Output_directory | ||
| run_CCS ${BAM_FILE} ${SAMPLE} ${WKD_ROOT}/1_isoseq3/1_ccs | ||
| run_LIMA ${SAMPLE} ${WKD_ROOT}/1_isoseq3/1_ccs ${WKD_ROOT}/1_isoseq3/2_lima "no_multiplex" | ||
| run_REFINE ${SAMPLE} ${WKD_ROOT}/1_isoseq3/2_lima ${WKD_ROOT}/1_isoseq3/3_refine | ||
| run_CLUSTER ${SAMPLE} ${WKD_ROOT}/1_isoseq3/3_refine ${WKD_ROOT}/1_isoseq3/4_cluster | ||
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| ##------------------------------------------------------------------------- | ||
| #run_star ${SAMPLE} ${RNASEQ_FILTERED_DIR} ${RNASEQ_MAPPED_DIR} |
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56
A_Global_Transcriptome/1_IsoSeq_Pipeline/2b_map_annotate_isoform.sh
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| #!/bin/bash | ||
| #SBATCH --export=ALL # export all environment variables to the batch job | ||
| #SBATCH -D . # set working directory to . | ||
| #SBATCH -p mrcq # submit to the parallel queue | ||
| #SBATCH --time=20:00:00 # maximum walltime for the job | ||
| #SBATCH -A Research_Project-MRC148213 # research project to submit under | ||
| #SBATCH --nodes=1 # specify number of nodes | ||
| #SBATCH --ntasks-per-node=16 # specify number of processors per node | ||
| #SBATCH --mail-type=END # send email at job completion | ||
| #SBATCH [email protected] # email address | ||
| #SBATCH --output=2b_map_annotate_isoform.o2 | ||
| #SBATCH --error=2b_map_annotate_isoform.e2 | ||
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| # J20 C20, C21, B21 and E18 Iso-Seq pipeline | ||
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| ##------------------------------------------------------------------------- | ||
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| # source config file and function script | ||
| module load Miniconda2/4.3.21 | ||
| SC_ROOT=/lustre/projects/Research_Project-MRC148213/lsl693/scripts/rTg4510/A_Global_Transcriptome | ||
| LOGEN_ROOT=/lustre/projects/Research_Project-MRC148213/lsl693/scripts/LOGen | ||
| source $SC_ROOT/1_IsoSeq_Pipeline/rTg4510_isoseq.config | ||
| source $SC_ROOT/1_IsoSeq_Pipeline/01_source_functions.sh | ||
| export PATH=$PATH:${LOGEN_ROOT}/miscellaneous | ||
| export PATH=$PATH:${LOGEN_ROOT}/assist_isoseq_processing | ||
| export PATH=$PATH:${LOGEN_ROOT}/assist_ont_processing | ||
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| J20_ALL_SAMPLE_NAMES=(B21 C20 C21 E18) | ||
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| ##------------------------------------------------------------------------- | ||
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| # merging_at_refine <input_flnc_bam_dir> <output_directory> <output_J20NAME> <samples.....> | ||
| #merging_at_refine $WKD_ROOT/1_isoseq3/3_refine $WKD_ROOT/1_isoseq3/5_merged_cluster ${J20NAME} ${J20_ALL_SAMPLE_NAMES[@]} | ||
| #refine2fasta $WKD_ROOT/1_isoseq3/3_refine ${J20_ALL_SAMPLE_J20NAMES[@]} | ||
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| # align individual samples | ||
| # run_pbmm2align <output_J20NAME> <clustered_dir> <mapped_dir> | ||
| #for i in ${J20_ALL_SAMPLE_NAMES[@]}; do run_pbmm2align $i $WKD_ROOT/1_isoseq3/4_cluster $WKD_ROOT/2_post_isoseq3/6_minimap; done | ||
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| # filter_alignment <J20NAME> <mapped_dir> | ||
| #for i in ${J20_ALL_SAMPLE_NAMES[@]}; do filter_alignment $i $WKD_ROOT/2_post_isoseq3/6_minimap; done | ||
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| # run_map_cupcakecollapse <sample_prefix_input/output_J20NAME> <isoseq3_input_directory> <mapping_output_directory> <tofu_output_directory> | ||
| #run_map_cupcakecollapse ${J20NAME} $WKD_ROOT/1_isoseq3/5_merged_cluster $WKD_ROOT/2_post_isoseq3/6_minimap $WKD_ROOT/2_post_isoseq3/7_tofu | ||
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| # demux <J20NAME> <refine_dir> <cluster_report> <tofu_dir> | ||
| #demux ${J20NAME} $WKD_ROOT/1_isoseq3/3_refine $WKD_ROOT/1_isoseq3/5_merged_cluster/${J20NAME}.clustered.cluster_report.csv $WKD_ROOT/2_post_isoseq3/7_tofu | ||
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| ##------------------------------------------------------------------------- | ||
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| source activate sqanti2_py3 | ||
| cd $WKD_ROOT/2_post_isoseq3/9_sqanti3 | ||
| python ${SQANTI3_DIR}/sqanti3_qc.py -t 30 $WKD_ROOT/2_post_isoseq3/7_tofu/${J20NAME}.collapsed.gff ${GENOME_GTF} ${GENOME_FASTA} --CAGE_peak ${CAGE_PEAK} --polyA_motif_list ${POLYA} --genename --isoAnnotLite --report skip &> ${J20NAME}.collapsed.sqanti.qc.log | ||
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