I have run tophat2 to align my paired-end rna-seq data to a reference genome:
/usr/bin/tophat2 -G ASgenome.gff3 -r 300 asgenome2 seq1.fa seq2.fa
and got results as ./tophat_out/accepted_hits.bam
Now I am reading the manual of cufflinks and have some questions about the option parameters:
1. what is the difference if I use -g ASgenome.gff3 or skip it? That is to say, will it be different between running
cufflinks -p8 -o clout ./tophat_out/accepted_hits.bam
and
cufflinks -p8 -g ASgenome.gff3 -o clout ./tophat_out/accepted_hits.bam
My purpose is to detect the new transcripts
2. cuffcompare results: class_code e
Should I remove those from final assembled geneset?
Any hints are welcome. Thanks a lot!
/usr/bin/tophat2 -G ASgenome.gff3 -r 300 asgenome2 seq1.fa seq2.fa
and got results as ./tophat_out/accepted_hits.bam
Now I am reading the manual of cufflinks and have some questions about the option parameters:
1. what is the difference if I use -g ASgenome.gff3 or skip it? That is to say, will it be different between running
cufflinks -p8 -o clout ./tophat_out/accepted_hits.bam
and
cufflinks -p8 -g ASgenome.gff3 -o clout ./tophat_out/accepted_hits.bam
My purpose is to detect the new transcripts
2. cuffcompare results: class_code e
Should I remove those from final assembled geneset?
Any hints are welcome. Thanks a lot!
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