Question: How to retrieve all the intron sequences and information (e.g. location) if I have a genome.
0
gravatar for biomoon
3.1 years ago by
biomoon10
biomoon10 wrote:

How to retrieve all the intron sequences and information (e.g. location) if I have a genome. Thanks in advance!

sequence next-gen genome • 1.3k views
ADD COMMENTlink modified 3.1 years ago by Antonio R. Franco4.0k • written 3.1 years ago by biomoon10
0
gravatar for dlyons
3.1 years ago by
dlyons0
dlyons0 wrote:

combine your exon and UTR files, then do a "bedtools intersect -v" against the gene file. everything remaining is intron (or at least this would be a good first guess).

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by dlyons0

Thanks. I have gtf file and a genome sequence. Bedtools can do that, right?

ADD REPLYlink written 3.1 years ago by biomoon10
0
gravatar for genomax
3.1 years ago by
genomax65k
United States
genomax65k wrote:

If it is one of the genomes available at UCSC/Ensembl you could use Table browser/BioMart (click on BioMart is top navigation bar) respectively to get that information.

ADD COMMENTlink written 3.1 years ago by genomax65k

Thank you. Good idea for a genome available in website. What I want is to get intron sequence from a new genome.

ADD REPLYlink written 3.1 years ago by biomoon10
0
gravatar for Antonio R. Franco
3.1 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

Look for a gff or gft file of your genome.

If no present, you can try some annotation using programs like genemark, August, et

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Antonio R. Franco4.0k

Thanks. I have got a gtf file using augustus. Can you tell me how to put all intron sequences to a single file? Thank you.

ADD REPLYlink written 3.1 years ago by biomoon10

Can you be more precise indicating what exactly do you want to get?

ADD REPLYlink written 3.1 years ago by Antonio R. Franco4.0k

@biomoon: If you have a GTF file then can you see annotations labelled as "introns"? You can use the answer in this thread to get the sequence: convert bed file to fasta file

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by genomax65k
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: 661 users visited in the last hour