Hello,
I have a paired-end RNAseq data set for two treatment conditions without any replicates. I want to check isoform variation in a particular gene and gene expression variations in general. Two paired-end file for each sample has been broken down in to seven files as the data was generated. I want to run these data in parallel using tuxedo suit.
The thing is I am not clear whether this tophat input command takes comma separated files as replicates or pieces of a single fastq file for two paired-end files.
tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]
And what would be the next steps in running tuxedo suite parallel ?
Could anyone please help me.
Thank you very much
TPH
I have a paired-end RNAseq data set for two treatment conditions without any replicates. I want to check isoform variation in a particular gene and gene expression variations in general. Two paired-end file for each sample has been broken down in to seven files as the data was generated. I want to run these data in parallel using tuxedo suit.
The thing is I am not clear whether this tophat input command takes comma separated files as replicates or pieces of a single fastq file for two paired-end files.
tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]
And what would be the next steps in running tuxedo suite parallel ?
Could anyone please help me.
Thank you very much
TPH
Comment