Comments (3)
Hi, the original idea was to generate an index based on the annotation, align the reads and discover new splicing sites. They will be then used to generate another (improved) index. Finally you'll use this index for aligning the reads. I think is ok to change the code since now everything can be done in a single step.
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I leave this to @lucacozzuto
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Thanks!
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Related Issues (20)
- picard.jar not found HOT 1
- Using Single end data HOT 5
- The genomeDir dir name is confusing
- GATK4 branch does not require separate Picard HOT 3
- suggest adding docker runOptions to nextflow.config HOT 1
- Cannot locate GATK.jar file HOT 1
- Error: Unable to access jarfile /scratch/oknjav001/transcriptomics/proteogenomics/variabtcalling/gatk/gatk3.7/GenomeAnalysisTK.jar HOT 1
- Reading single end reads HOT 4
- Whether do not generate star index if provide directly? HOT 1
- Process POST_PROCESS_VCF failes when order of chromosomes in result.DP8.vcf differs from that in the GRCm38/Annotation/Variation/Mus_musculus.vcf
- could not execute mkdir HOT 1
- mm39 variants / black list HOT 4
- will there be a nf of dna variant calling which need paired samples
- Could not build fai index genome.fa.fai
- denylisted genome file
- Documentation issue? HOT 2
- Process `ASE_KNOWNSNPS (SAMPLE123XYZ)` terminated with an error exit status (2) (More then one variant context at position: chr3:XXXXXXX) HOT 2
- Operator `phase` is deprecated
- ERROR: Input files reference and features have incompatible contigs
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