gff和gtf格式都可以储存基因信息，但是不同的软件对于文件格式的要求不同。
关于gff文件和gtf格式的详细介绍，可以参见生信技能树，简单的区别对比见下表。
http://www.biotrainee.com/thread-2705-1-1.html
有时gff和gtf需要转换，本篇本章主要介绍gffread。gffread是Cufflinks的子功能，Cufflinks程序从RNA-Seq数据中组装转录组，并量化它们的表达。
Cufflinks官网：
http://cole-trapnell-lab.github.io/cufflinks/
说明书：
https://github.com/cole-trapnell-lab/cufflinks/blob/master/README.md
1.下载安装
1.1 依赖环境
1.1.1 Boost
- Mac OS X
bjam --prefix=<YOUR_BOOST_INSTALL_DIRECTORY> --toolset=darwin architecture=x86 address_model=32_64 link=static runtime-link=static --layout=versioned stage install
- 32位 Linux系统
bjam --prefix=<YOUR_BOOST_INSTALL_DIRECTORY> --toolset=gcc architecture=x86 address_model=32 link=static runtime-link=static stage install
- 64位 Linux 系统
bjam --prefix=<YOUR_BOOST_INSTALL_DIRECTORY> --toolset=gcc architecture=x86 address_model=64 link=static runtime-link=static stage install
1.1.2 SAM tools
http://samtools.sourceforge.net/
1.1.3 Eigen libraries
https://eigen.tuxfamily.org/index.php?title=Main_Page
1.2 下载
选择合适的版本下载压缩包，下载地址：
http://cole-trapnell-lab.github.io/cufflinks/install/
1.3 安装
$ tar xvf cufflinks-2.2.1.Linux_x86_64.tar.gz
1.4 检测
$ cd ~/cufflinks-2.2.1.Linux_x86_64
$ gffread -h
1.5 添加环境变量
$ vim ~/.bashrc
export PATH= ~/cufflinks-2.2.1.Linux_x86_64:$PATH
$ source ~/.bashrc
2.gffread功能
说明书：
http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
2.1 gff转gtf
$ gffread -T CE10g_v2.0.gff3 -o CE10g_v2.0.gtf
2.2 对gtf文件快速检查
$ gffread -E CE10g_v2.0.gtf -o- | less
2.3 对gff文件快速检查
$ gffread -E CE10g_v2.0.gff3 -T -o- | more
2.4 评估转录本发现的准确性
$ gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf
2.5 gtf转gff
$ gffread -L CE10g_v2.0.gtf -o v2.0.gff
2.6 查看gffread具体参数
$ gffread -h
Usage:
gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>]
[-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]
[-CTVNJMKQAFGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
[-i <maxintron>]
Filters and/or converts GFF3/GTF2 records.
<input_gff> is a GFF file, use '-' if the GFF records will be given at stdin
Options:
-g full path to a multi-fasta file with the genomic sequences
for all input mappings, OR a directory with single-fasta files
(one per genomic sequence, with file names matching sequence names)
-s <seq_info.fsize> is a tab-delimited file providing this info
for each of the mapped sequences:
<seq-name> <seq-length> <seq-description>
(useful for -A option with mRNA/EST/protein mappings)
-i discard transcripts having an intron larger than <maxintron>
-r only show transcripts overlapping coordinate range <start>..<end>
(on chromosome/contig <chr>, strand <strand> if provided)
-R for -r option, discard all transcripts that are not fully
contained within the given range
-U discard single-exon transcripts
-C coding only: discard mRNAs that have no CDS feature
-F full GFF attribute preservation (all attributes are shown)
-G only parse additional exon attributes from the first exon
and move them to the mRNA level (useful for GTF input)
-A use the description field from <seq_info.fsize> and add it
as the value for a 'descr' attribute to the GFF record
-O process also non-transcript GFF records (by default non-transcript
records are ignored)
-V discard any mRNAs with CDS having in-frame stop codons
-H for -V option, check and adjust the starting CDS phase
if the original phase leads to a translation with an
in-frame stop codon
-B for -V option, single-exon transcripts are also checked on the
opposite strand
-N discard multi-exon mRNAs that have any intron with a non-canonical
splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
-J discard any mRNAs that either lack initial START codon
or the terminal STOP codon, or have an in-frame stop codon
(only print mRNAs with a fulll, valid CDS)
--no-pseudo: filter out records matching the 'pseudo' keyword
-M/--merge : cluster the input transcripts into loci, collapsing matching
transcripts (those with the same exact introns and fully contained)
-d <dupinfo> : for -M option, write collapsing info to file <dupinfo>
--cluster-only: same as --merge but without collapsing matching transcripts
-K for -M option: also collapse shorter, fully contained transcripts
with fewer introns than the container
-Q for -M option, remove the containment restriction:
(multi-exon transcripts will be collapsed if just their introns match,
while single-exon transcripts can partially overlap (80%))
--force-exons: make sure that the lowest level GFF features are printed as
"exon" features
-E expose (warn about) duplicate transcript IDs and other potential
problems with the given GFF/GTF records
-D decode url encoded characters within attributes
-Z merge close exons into a single exon (for intron size<4)
-w write a fasta file with spliced exons for each GFF transcript
-x write a fasta file with spliced CDS for each GFF transcript
-W for -w and -x options, also write for each fasta record the exon
coordinates projected onto the spliced sequence
-y write a protein fasta file with the translation of CDS for each record
-L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
-m <chr_replace> is a reference (genomic) sequence replacement table with
this format:
<original_ref_ID> <new_ref_ID>
GFF records on reference sequences that are not found among the
<original_ref_ID> entries in this file will be filtered out
-o the "filtered" GFF records will be written to <outfile.gff>
(use -o- for printing to stdout)
-t use <trackname> in the second column of each GFF output line
-T -o option will output GTF format instead of GFF3
引用转载请注明出处，如有错误敬请指出。
网友评论