Commit 6a559a60 authored by psimion's avatar psimion
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MAJ readme to v1.2 (3)

parent 5cf4e9d0
......@@ -369,12 +369,16 @@ docker run -t -i -P -v /home/user/where/data/are:/CroCoData:rw crocodock /bin/b
The transcriptome fasta files and their corresponding fastq files to be analyzed must be present in a given directory specified by the user with the option `--in` [short: -i]. Croco will then look for a configuration file specified with the option `--cnf` [short: -k] to get the list of files to use. The format of this configuration file is as follows:
**for paired-end reads**
species_A.fasta forward-reads-for-speciesA.fastq reverse-reads-for-speciesA.fastq
species_B.fasta forward-reads-for-speciesB.fastq reverse-reads-for-speciesB.fastq
species_A.fasta forward-reads-for-speciesA.fastq reverse-reads-for-speciesA.fastq
species_B.fasta forward-reads-for-speciesB.fastq reverse-reads-for-speciesB.fastq
**for unpaired reads** :
species_A.fasta reads-for-speciesA.fastq
species_B.fasta reads-for-speciesB.fastq
species_A.fasta reads-for-speciesA.fastq
species_B.fasta reads-for-speciesB.fastq
Things to remember when preparing input files :
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