Hi!
I have several different samples that I have been running tophat and cufflinks on, and I am now doing cuffmerge on the end result of this. My goal is to get a transcriptome fasta file at the end.
I have used the following commands:
tophat2 --b2-very-sensitive -p num -r num --mate-std-dev num --library-type fr-unstranded -G genome.gtf --transcriptome-index=indexfile -o outputdir referencegenome 1.fastq 2.fastq
followed by cufflinks without any options, i.e.
cufflinks -p 22 -o newoutput outputdir/accepted_hits.bam
So, now I am at the stage where I want to merge these things, and I have questions:
1. what is the difference between merged.gtf and transcripts.gtf?
2. what happens if I also include a reference gtf file with the -g option?Is it incorporated in the same way as the other gtf files, or is it only used for naming?
3. what happens if I include the referencegenome with the -s option?
Thanks!
I have several different samples that I have been running tophat and cufflinks on, and I am now doing cuffmerge on the end result of this. My goal is to get a transcriptome fasta file at the end.
I have used the following commands:
tophat2 --b2-very-sensitive -p num -r num --mate-std-dev num --library-type fr-unstranded -G genome.gtf --transcriptome-index=indexfile -o outputdir referencegenome 1.fastq 2.fastq
followed by cufflinks without any options, i.e.
cufflinks -p 22 -o newoutput outputdir/accepted_hits.bam
So, now I am at the stage where I want to merge these things, and I have questions:
1. what is the difference between merged.gtf and transcripts.gtf?
2. what happens if I also include a reference gtf file with the -g option?Is it incorporated in the same way as the other gtf files, or is it only used for naming?
3. what happens if I include the referencegenome with the -s option?
Thanks!