Creating Transcriptome File for Use With BWA from GTF file and genomic fasta file

PolPittacus7 · 05-19-2015, 03:48 AM

I downloaded the Mus musculus mm10 pre-built tophat indices from the Tophat website (http://ccb.jhu.edu/software/tophat/igenomes.shtml). This package comes with a .gtf file that specifies junction boundaries and start/stop codon positions. It also contains a .fa file for the mouse genome.

I would like to produce a .fa file that contains all of the mouse RNA transcript sequences from the above two files. Is there any software that does this? I have read of de novo transcriptome assembly software like Trinity, but I do not think it would be ideal for what I would like to do here. I merely need some kind of script/tool to generate the annotated mRNA (and ideally, rRNA, mtRNA, and ncRNA) sequences that will match the annotation in the aforementioned two files (.gtf and .fa from the tophat pre-built index).

Thank you kindly for your time and help. Please let me know if there is any further information you would like to help evaluate my query. If I do find an appropriate tool for this problem, I plan on writing a script to extract and splice necessary sequences from the genomic .fa file, and will upload this script for others to use (but would rather avoid re-inventing the wheel if possible!).

jp. · 07-16-2015, 03:18 AM

Hi
Any solution of your problem ?
I am confused with too

westerman · 07-16-2015, 07:39 AM

Whenever I heard the word "gtf" or "vcf" then my mind goes to BEDtools. And indeed one of the programs is "fastaFromBed" which "Creates FASTA sequences based on intervals in a BED/GFF/VCF file." GTF is just a GFF in disguise.

jp. · 07-17-2015, 10:19 AM

Thanks westerman, however, I like to ask you something different but relative.
After running Denovo Trinity reports Trinity.fasta and then I did blast got blastx.outfmt6. I also have TransDecoder output i.e. Trinity.fasta.transdecoder.cds , Trinity.fasta.transdecoder.gff3 , Trinity.fasta.transdecoder.mRNA , Trinity.fasta.transdecoder.pep

I am confused how to add real gene names in to Trinity.fasta So that Trinity numbered genes (TR1...n) will be replaced by real gene names which are available in Trinity.fasta.transdecoder.gff3 or blastx.outfmt6 ?
Any idea ?

westerman · 07-17-2015, 10:45 AM

Quote:

Originally Posted by jp.

Thanks westerman, however, I like to ask you something different but relative.
After running Denovo Trinity reports Trinity.fasta and then I did blast got blastx.outfmt6. I also have TransDecoder output i.e. Trinity.fasta.transdecoder.cds , Trinity.fasta.transdecoder.gff3 , Trinity.fasta.transdecoder.mRNA , Trinity.fasta.transdecoder.pep

I am confused how to add real gene names in to Trinity.fasta So that Trinity numbered genes (TR1...n) will be replaced by real gene names which are available in Trinity.fasta.transdecoder.gff3 or blastx.outfmt6 ?
Any idea ?

No idea. This is processing step that I do not use thus am unable to give advice.

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05-19-2015, 03:48 AM	#1
PolPittacus7 Junior Member Location: United Kingdom Join Date: Mar 2015 Posts: 5	Creating Transcriptome File for Use With BWA from GTF file and genomic fasta file I downloaded the Mus musculus mm10 pre-built tophat indices from the Tophat website (http://ccb.jhu.edu/software/tophat/igenomes.shtml). This package comes with a .gtf file that specifies junction boundaries and start/stop codon positions. It also contains a .fa file for the mouse genome. I would like to produce a .fa file that contains all of the mouse RNA transcript sequences from the above two files. Is there any software that does this? I have read of de novo transcriptome assembly software like Trinity, but I do not think it would be ideal for what I would like to do here. I merely need some kind of script/tool to generate the annotated mRNA (and ideally, rRNA, mtRNA, and ncRNA) sequences that will match the annotation in the aforementioned two files (.gtf and .fa from the tophat pre-built index). Thank you kindly for your time and help. Please let me know if there is any further information you would like to help evaluate my query. If I do find an appropriate tool for this problem, I plan on writing a script to extract and splice necessary sequences from the genomic .fa file, and will upload this script for others to use (but would rather avoid re-inventing the wheel if possible!).

07-16-2015, 03:18 AM	#2
jp. Senior Member Location: NikoNarita.jp Join Date: Jul 2013 Posts: 142	Hi Any solution of your problem ? I am confused with too

07-16-2015, 07:39 AM	#3
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	Whenever I heard the word "gtf" or "vcf" then my mind goes to BEDtools. And indeed one of the programs is "fastaFromBed" which "Creates FASTA sequences based on intervals in a BED/GFF/VCF file." GTF is just a GFF in disguise.

07-17-2015, 10:19 AM	#4
jp. Senior Member Location: NikoNarita.jp Join Date: Jul 2013 Posts: 142	Thanks westerman, however, I like to ask you something different but relative. After running Denovo Trinity reports Trinity.fasta and then I did blast got blastx.outfmt6. I also have TransDecoder output i.e. Trinity.fasta.transdecoder.cds , Trinity.fasta.transdecoder.gff3 , Trinity.fasta.transdecoder.mRNA , Trinity.fasta.transdecoder.pep I am confused how to add real gene names in to Trinity.fasta So that Trinity numbered genes (TR1...n) will be replaced by real gene names which are available in Trinity.fasta.transdecoder.gff3 or blastx.outfmt6 ? Any idea ?