"tofu_wrap.py" can divides input into different size bins, runs clustering on the individual bins and combines them later.The question is that there is no 'combined/' subdirectory in tofu_wrap output result.So,i can't get final output files i want to work with.
The command i used is below:
tofu_wrap.py --nfl_fa isoseq_nfl.fasta --ccs_fofn reads_of_insert.fofn --bas_fofn input.fofn -d clusterOut --quiver --gmap_db /zs32/data-analysis /liucy_group /llhuang/Reflib/gmapdb --gmap_name hg19 isoseq_flnc.fasta final.consensus.fa Because of my sever is high-powered single-node computer, I can't install SGE successfully and therefore don't select parameter '--use_sge'. I don't know whether this is the cause of the problem. By the way, I've already tried to add '--bin_manual' back in my command following Bowhan's advice(thank you),but it still only have no 'combined/' subdirectory in output files. There are "
0to1kb/
1to2kb/
2to3kb/
3to4kb/
4to5kb/
fasta_fofn_files/" in the directory clusterOut.
Moreover, what should i do next if i run "tofu_wrap.py" successfully. I want to obtain the difference of transcripts from the third sequencing data between human and mouse.
Any advice will be appreciated, thank you in advance!
The command i used is below:
tofu_wrap.py --nfl_fa isoseq_nfl.fasta --ccs_fofn reads_of_insert.fofn --bas_fofn input.fofn -d clusterOut --quiver --gmap_db /zs32/data-analysis /liucy_group /llhuang/Reflib/gmapdb --gmap_name hg19 isoseq_flnc.fasta final.consensus.fa Because of my sever is high-powered single-node computer, I can't install SGE successfully and therefore don't select parameter '--use_sge'. I don't know whether this is the cause of the problem. By the way, I've already tried to add '--bin_manual' back in my command following Bowhan's advice(thank you),but it still only have no 'combined/' subdirectory in output files. There are "
0to1kb/
1to2kb/
2to3kb/
3to4kb/
4to5kb/
fasta_fofn_files/" in the directory clusterOut.
Moreover, what should i do next if i run "tofu_wrap.py" successfully. I want to obtain the difference of transcripts from the third sequencing data between human and mouse.
Any advice will be appreciated, thank you in advance!
Comment