Question: Mapping of De novo assembled transcripts to draft genome
0
gravatar for Bioinfonext
3.3 years ago by
Bioinfonext220
Korea
Bioinfonext220 wrote:

I want to map de novo assembled transcript which is in full length (start codon to stop codon) to the draft genome and want to extract partially mapped or unmapped transcript.

I also want to discard chimeric transcripts.

Please help me to improve the gmap command line:

/home/software/gmap-2016-11-07/src/gmap -D /home/database -d Genome Trinity.fasta --chimera-margin=0 --min-trimmed-coverage=90 --min-identity=95 --failed-input /home/yog/failed.fasta

Will --chimera-margin=0 discard chimeric transcripts?

--min-trimmed-coverage=90 help to put all transcripts in failed.fasta which not able to cover 90% coding sequence of a gene?

--failed-input is these are the transcripts which do not completely map on genome according to above criteria?

**The genome which is I am using here is draft genome ...do not contain all the gene sequences and some of the gene sequences partially present in the draft genome.

Thanks

rna-seq • 858 views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Bioinfonext220
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1206 users visited in the last hour