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Commit 366a0d55 authored by cbedet's avatar cbedet
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modif of gff file to correct the bug in htseq count (gtf format)

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src/RNAseq_cec.sh
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# grep WormBase c_elegans.PRJNA13758.WS278.annotations.gff3 > c_elegans.PRJNA13758.WS278.wormbase.gff3
./nextflow run src/RNAseq_cec.nf \ ./nextflow run src/RNAseq_cec.nf \
-profile psmn \ -profile psmn \
--fastq "subset/*_R{1,2}.fastq.gz" \ --fastq "subset/*_R{1,2}.fastq.gz" \
--cds_fasta "data/c_elegans.PRJNA13758.WS278.all_transcripts.fa" \ --cds_fasta "data/c_elegans.PRJNA13758.WS278.all_transcripts.fa" \
--genomic_fasta "data/c_elegans.PRJNA13758.WS278.genomic.fa" \ --genomic_fasta "data/c_elegans.PRJNA13758.WS278.genomic.fa" \
--genomic_gff3 "data/c_elegans.PRJNA13758.WS278.annotations.gff3" \ --genomic_gff3 "data/c_elegans.PRJNA13758.WS278.wormbase.gff3" \
-resume -resume
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