How to map genome guided assembly TRANSCRIPTS to Genome and extract the longest one for each genome locus

Question

[Bioinfonext]

Hi,

I did genome guided assembly using StringTie, It generate multiple isoforms, Can you please suggest how i can map these transcripts to genome again, to get only single accurately assembled transcripts for each locus.

Thanks

Answer 1

[Rohit]

From your comments I think what you want is redundancy removal. This can be done with -

1) Without the reference using Vmatch or CD-hit or uclust without the need of a reference - combine both denovo and genome guided assembly transcripts and take only the longest from the superset removing complete overlapping regions.

2) Use the reference to map the transcripts with a split-aware mapper and keep only the longest one in the region when they are overlapping subsets.

[Bioinfonext]

1)take only the longest from the superset removing complete overlapping regions? Please suggest if any tool is available, do you think CD-HIT is useful here.

2) Use the reference to map the transcripts with a split-aware mapper and keep only the longest one in the region when they are overlapping subsets.

What about second step, how can I do it?

[Rohit]

1) Vmatch or CD-hit or uclust - These are all tools to keep the longest sequences. The commands for vmatch are as follows (these were 2 years old, not sure if there are changes) -

mkvtree -allout -pl -db sequences.fasta -dna -indexname dbname 
vmatch -d -p -dbcluster 100 0 -v -nonredundant nr_sequences.fa dbname

2) You can use GMAP or bwa-mem to map the sequences at high identity. Then use bedtools (cluster) or kent-utilities (bedRemoveOverlap) to remove the subsets or completely overlapping sequences.