{"id":947,"date":"2024-10-16T11:15:41","date_gmt":"2024-10-16T03:15:41","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=947"},"modified":"2024-10-28T17:42:24","modified_gmt":"2024-10-28T09:42:24","slug":"%e5%9f%ba%e5%9b%a0%e7%bb%84%e5%8a%9f%e8%83%bd%e9%a2%84%e6%b5%8b","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2024\/10\/16\/%e5%9f%ba%e5%9b%a0%e7%bb%84%e5%8a%9f%e8%83%bd%e9%a2%84%e6%b5%8b\/","title":{"rendered":"\u57fa\u56e0\u7ec4\u7ed3\u6784\u9884\u6d4b"},"content":{"rendered":"\t\t
\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

\u57fa\u56e0\u7ec4\u7ed3\u6784\u9884\u6d4b<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

\u5f15\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

\u57fa\u56e0\u7ec4\u7684\u7ed3\u6784\u6ce8\u91ca\u76ee\u524d\u5df2\u7ecf\u6709\u5f88\u591a\u7684\u6d41\u7a0b\uff0c\u57fa\u672c\u4e0a\u90fd\u662f\u7ed3\u5408\u8f6c\u5f55\u7ec4+\u86cb\u767d+\u4ece\u5934\u9884\u6d4b\u4e09\u65b9\u8bc1\u636e\u8fdb\u884c\u6574\u5408\u6ce8\u91ca\u3002\u56e0\u6b64\uff0c\u672c\u6b21\u7684\u7ed3\u6784\u6ce8\u91ca\u9009\u62e9Augustus\uff08\u4ece\u5934\u9884\u6d4b\uff09+Miniprot\uff08\u86cb\u767d\uff09+PASA&hisat2&Trinity\uff08\u8f6c\u5f55\u7ec4\uff09\u5b8c\u6210\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

1. \u8f6f\u4ef6\u4e0b\u8f7d<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

mamba create -n Gene_Anno<\/p>

mamba activate Gene_Anno<\/p>\n

# \u8f6c\u5f55\u7ec4\u76f8\u5173<\/p>\n

mamba install bioconda::hisat2<\/p>\n

mamba install bioconda::trinity<\/p>\n

mamba install bioconda::stringtie<\/p>\n

mamba install bioconda::pasa<\/p>\n

mamba install bioconda::samtools<\/span><\/p>\n

# \u86cb\u767d\u6ce8\u91ca<\/p>\n

mamba install bioconda::miniprot<\/p>\n

# \u4ece\u5934\u9884\u6d4b<\/p>\n

mamba install bioconda::augustus<\/p>\n

# \u8bc1\u636e\u6574\u5408<\/p>\n

mamba install bioconda::evidencemodeler<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

2. \u8f6f\u4ef6\u4f7f\u7528<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

2.1 \u8f6c\u5f55\u7ec4\u90e8\u5206<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

hisat2\u6bd4\u5bf9<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

hisat2-build genome.fasta ref<\/p>\n

# \u6bd4\u5bf9\u548c\u6392\u5e8f<\/span><\/p>\n

hisat2 --new-summary --summary-file rnaseq.hisat.summary --threads 10 -x ref -1 rnaseq_1.fastq.gz -2 rnaseq_2.fastq.gz | samtools sort -@ 5 -o rnaseq.bam -<\/h5>\n

samtools index rnaseq.bam<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

\u4f7f\u7528Trinity\u57fa\u4e8e\u6bd4\u5bf9\u7684bam\u6587\u4ef6\u8fdb\u884c\u8f6c\u5f55\u7ec4\u7684\u7ec4\u88c5<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

Trinity --max_memory 100G --genome_guided_bam .\/rnaseq.bam --genome_guided_max_intron 20000 --CPU 10<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

\u8fd0\u884cPASA\uff0c\u7b2c\u4e00\u6b65\u8981\u4fee\u6539PASA\u7684\u914d\u7f6e\u6587\u4ef6<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

## templated variables to be replaced exist as <__var_name__><\/p>\n

# database settings
DATABASE=\/tmp\/Bra-pasa.sqlite # \u6570\u636e\u5e93\u7684\u8def\u5f84\uff0c\u4e5f\u662f\u552f\u4e00\u9700\u8981\u786c\u6027\u4fee\u6539\u7684\u5730\u65b9\uff0c\u4fee\u6539\u6210\u4f60\u81ea\u5df1\u6570\u636e\u7684\u8def\u5f84<\/p>\n

#######################################################
# Parameters to specify to specific scripts in pipeline
# create a key = \"script_name\" + \":\" + \"parameter\"
# assign a value as done above.<\/p>\n

#script validate_alignments_in_db.dbi
validate_alignments_in_db.dbi:--MIN_PERCENT_ALIGNED=80
validate_alignments_in_db.dbi:--MIN_AVG_PER_ID=95<\/p>\n

#script subcluster_builder.dbi
subcluster_builder.dbi:-m=50<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

\u8fd0\u884cPASA pipline<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

### PASA pipline<\/p>\n

Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g .\/genome.fasta -t transcript.fasta --ALIGNERS minimap2 --CPU 10\u00a0<\/p>\n

#\u53c2\u6570<\/p>\n

# -c<\/b> \u914d\u7f6e\u6587\u4ef6\u00a0<\/p>\n

# -g<\/b> \u57fa\u56e0\u7ec4\u6587\u4ef6\u00a0<\/p>\n

# -t<\/b> \u8f6c\u5f55\u672c\u6587\u4ef6\u00a0<\/p>\n

# --ALIGENERS<\/b> \u6bd4\u5bf9\u7684\u8f6f\u4ef6\u00a0<\/p>\n

# --CPU<\/b> \u8fd0\u884c\u7684\u7ebf\u7a0b\u6570<\/p>\n

# -C<\/b> \u4ece\u5934\u521b\u5efa\u6570\u636e\u5e93<\/p>\n

# -R<\/b> \u8fd0\u884c\u7ec4\u88c5\u548c\u6bd4\u5bf9<\/p>\n

# \u8f93\u51fa\u7ed3\u679c<\/p>\n

.pasa_assemblies.gff3\uff1a<\/strong>\u6700\u91cd\u8981\u7684\u8f93\u51fa\u7ed3\u679c\uff0c\u6700\u540eEVM\u8bc1\u636e\u6574\u5408\u7528\u5230\u7684\u8f93\u5165\u6587\u4ef6<\/p>\n

.assemblies.fasta\uff1a<\/strong>PASA\u7684\u7ec4\u88c5\u7ed3\u679c<\/p>\n

\u00a0<\/strong><\/p>\n

# PASA\u672c\u5f88\u8fd8\u652f\u6301\u8c03\u7528Transdecoder\u5bf9\u7ed3\u679c\u8fdb\u884c\u6210cds\u548cpep\u7684\u9884\u6d4b<\/p>\n

\/usr\/local\/src\/PASApipeline\/scripts\/pasa_asmbls_to_training_set.dbi --pasa_transcripts_fasta Bra-pasa.sqlite.assemblies.fasta --pasa_transcripts_gff3 Bra-pasa.sqlite.pasa_assemblies.gff3<\/p>\n

#\u00a0<\/b>--pasa_transcripts_fasta <\/b>PASA\u7684\u7ec4\u88c5\u7ed3\u679c<\/p>\n

# --pasa_transcripts_gff3 <\/b>PASA\u7684gff3\u683c\u5f0f\u7684\u8f93\u51fa\u7ed3\u679c<\/p>\n

# \u8f93\u51fa\u7ed3\u679c<\/p>\n

# .transdecoder.bed <\/strong>bed\u6587\u4ef6<\/p>\n

# .transdecoder.cds <\/strong>\u9884\u6d4b\u7684cds\u6587\u4ef6<\/p>\n

# .transdecoder.pep <\/strong>\u9884\u6d4b\u7684pep\u6587\u4ef6<\/p>\n

# .transdecoder.gff3 <\/strong>\u5e26\u6709cds\u7684gff3\u6587\u4ef6<\/p>\n

# .transdecoder.genome.bed <\/strong>\u8f6c\u6362\u6210\u57fa\u56e0\u7ec4\u5e8f\u5217ID\u7684bed\u6587\u4ef6<\/p>\n

# .transdecoder.genome.gff3 <\/strong>\u8f6c\u6362\u6210\u57fa\u56e0\u7ec4\u5e8f\u5217ID\u7684gff3\u6587\u4ef6 \u540e\u7eedEVM\u7684\u8f93\u5165\u6587\u4ef6<\/b><\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

2.2 \u86cb\u767d\u90e8\u5206<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

miniprot\u6bd4\u5bf9<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

# \u5c06\u4e0b\u8f7d\u7684\u591a\u4e2a\u8fd1\u7f18\u7269\u79cd\u7684\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u5408\u5e76<\/p>\n

cat 1_pep.fasta 2_pep.fasta > total_pep.fasta<\/p>\n

# \u8fd0\u884cminiprot<\/p>\n

miniprot -I -t 10 --gff --outc 0.5 --outn 100 .genome.fasta total_pep.fasta > miniprot.gff<\/p>\n

# \u53c2\u6570<\/p>\n

# -I \u8ba1\u7b97\u5185\u542b\u5b50\u6700\u5927\u957f\u5ea6\u7684\u9608\u503c<\/p>\n

# -t \u7ebf\u7a0b\u6570<\/p>\n

# --gff \u751f\u6210gff3\u683c\u5f0f\u7684\u7ed3\u679c<\/p>\n

# --outc \u6bd4\u5bf9\u7684\u767e\u5206\u6bd4\u9608\u503c<\/p>\n

# --outn \u6bd4\u5bf9\u7684\u8f93\u51fa\u7ed3\u679c\u9608\u503c<\/p>\n

# \u8f93\u51fa\u7ed3\u679c<\/p>\n

miniprot.gff\uff1a<\/b>\u00a0\u6bd4\u5bf9\u7684gff3\u683c\u5f0f\u7684\u7ed3\u679c\uff0c\u540e\u7eed\u8f93\u5982\u5230EVM<\/b><\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

2.3 \u4ece\u5934\u9884\u6d4b\n<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

\u8bad\u7ec3\u6a21\u578b\uff08\u53ef\u9009\u6b65\u9aa4\uff0c\u5982\u679cAugustus\u4e2d\u6709\u8fd1\u7f18\u7269\u79cd\u7684\u6a21\u578b\uff0c\u53ef\u4ee5\u76f4\u63a5\u5e94\u7528\uff09<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

# \u8bad\u7ec3\u6a21\u578b<\/p>\n

autoAugTrain.pl --genome genome.fasta --trainingset training.gff --species=Test2 --optrounds=5 --cpus=10
-v -v -v<\/p>\n

# \u53c2\u6570<\/p>\n

# --genome \u57fa\u56e0\u7ec4\u6587\u4ef6<\/p>\n

# --trainingset \u7528\u4f5c\u8bad\u7ec3\u7684\u8bad\u7ec3\u96c6\u6570\u636e<\/p>\n

# --species \u751f\u6210\u7684\u8bad\u7ec3\u6a21\u578b\u7684\u540d\u5b57\uff0c\u81ea\u5df1\u5236\u5b9a<\/p>\n

# --optrounds \u4f18\u5316\u8f6e\u6570<\/p>\n

# --cpus \u8fd0\u884c\u7684\u7ebf\u7a0b\u6570<\/p>\n

# -v -v -v \u65e5\u5fd7\u7684\u8f93\u51fa\u8be6\u7ec6\u7a0b\u5ea6 3\u4e2a -v\u5219\u662f\u6700\u8be6\u7ec6<\/p>\n

# \u8f93\u51fa\u7ed3\u679c<\/p>\n

# autoAugTrain<\/b>\uff1a \u5305\u542b\u4e86\u8bad\u7ec3\u8fc7\u7a0b\u7684\u8fc7\u7a0b\u6587\u4ef6\u548c\u6700\u540e\u7684\u6a21\u578b<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

\u8fd0\u884cAugustus\uff08\u5355\u7ebf\u7a0b\uff09<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

# \u76f4\u63a5\u8fd0\u884cAugustus<\/p>\n

augustus --species=Test2 --genemodel=complete --softmasking=1 --codingseq=on --exonnames=on --outfile=augustus.gff --errfile=augustus.err genome.sm.fasta<\/p>\n

# \u53c2\u6570<\/p>\n

# --species<\/b> \u9884\u6d4b\u4f7f\u7528\u7684\u6a21\u578b<\/p>\n

# --genemodel<\/b> \u53ea\u4fdd\u7559\u5b8c\u6574\u9884\u6d4b\u7684\u57fa\u56e0<\/p>\n

# --softmasking<\/b> \u662f\u5426\u4f7f\u7528\u8f6f\u5c4f\u853d\u540e\u7684\u57fa\u56e0\u5e8f\u5217<\/p>\n

# --codingseq<\/b> \u7ed3\u679c\u4e2d\u8f93\u51faCDS\u5e8f\u5217<\/p>\n

# --exonnames<\/b> \u7ed3\u679c\u4e2d\u8f93\u51fa\u5916\u663e\u5b50\u540d\u79f0<\/p>\n

# --outfile<\/b> \u8f93\u51fa\u6587\u4ef6\u540d<\/p>\n

# --errfile<\/b> \u8f93\u51fa\u7684\u62a5\u9519\u4fe1\u606f\u6587\u4ef6<\/p>\n

# \u8f93\u51fa\u6587\u4ef6<\/p>\n

augustus.gff\uff1a<\/b>\u9884\u6d4b\u7ed3\u679c<\/p>\n

 <\/p>\n

# Augustus \u8fd8\u652f\u6301\u6dfb\u52a0\u5176\u4ed6\u7684\u8bc1\u636e\u4fe1\u606f\u8fdb\u884c\u9884\u6d4b\uff08\u4f8b\u5982\u8f6c\u5f55\u7ec4\uff09<\/p>\n

# bam\u6587\u4ef6\u8f6c\u5316\u4e3aAugustus\u7684\u8bc1\u636e\u683c\u5f0f<\/p>\n

bam2hints --in=..\/01.RNAseq\/rnaseq.bam --out=hints.gff<\/p>\n

# \u8fd0\u884cAugustus<\/p>\n

augustus --species=Test2 --hintsfile=hints.gff --extrinsicCfgFile=~\/augustus_config\/extrinsic\/extrinsic.M.RM.E.W.cfg --genemodel=complete --softmasking=1 --codingseq=on --exonnames=on --outfile=augustus.gff --errfile=augustus.err genome.sm.fasta<\/p>\n

 <\/p>\n

# \u5f97\u5230gff\u6587\u4ef6\u540e\uff0c\u8fd8\u53ef\u4ee5\u628a\u9884\u6d4b\u7684CDS\u548cPEP\u5e8f\u5217\u76f4\u63a5\u63d0\u524d\u51fa\u6765<\/p>\n

getAnnoFasta.pl --seqfile genome.sm.fasta augustus.gff<\/p>\n

# \u8f93\u51fa\u7ed3\u679c<\/p>\n

# .aa<\/strong> PEP\u5e8f\u5217<\/p>\n

# .codingseq<\/strong> CDS\u5e8f\u5217<\/p>\n

# .cdsexons<\/strong> \u5916\u663e\u5b50\u5e8f\u5217<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

\u591a\u7ebf\u7a0b\u5e76\u884c\u8fd0\u884cAugustus<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

# \u5207\u5206\u57fa\u56e0\u7ec4\uff08\u6309\u5e8f\u5217\uff09<\/p>\n

seqkit split -i -O split genome.sm.fasta<\/p>\n

 <\/p>\n

# \u751f\u6210Augustus\u6307\u5b9a\u7684\u5e8f\u5217\u6587\u4ef6\u5217\u8868<\/p>\n

ls split\/*.fasta | while read f ;do seqkit fx2tab -i -n -l $f |awk '{print \"'$f'\\t1\\t\" $2}'; done > chr.list<\/p>\n

 <\/p>\n

# \u751f\u6210\u5e76\u884c\u7684Augustus\u8fd0\u884c\u547d\u4ee4<\/p>\n

createAugustusJoblist.pl --sequences=chr.list --wrap=\"#\" --overlap=100000 --chunksize=10000000 --outputdir=.\/augDir --joblist=jobs.lst --jobprefix=augSplit_ --command \"augustus --species=Test1 --extrinsicCfgFile=.\/extrinsic.cfg --hintsfile=hints.gff --genemodel=complete --softmasking=1 --codingseq=on --exonnames=on \"<\/p>\n

# \u53c2\u6570<\/p>\n

--sequences<\/b>=chr.list \u57fa\u56e0\u7ec4\u5e8f\u5217\u6587\u4ef6\u4fe1\u606f<\/p>\n

--wrap<\/b>=\"#\" \u8fd0\u884c\u811a\u672c\u7684\u7c7b\u578b\uff0c\u56e0\u4e3a\u6211\u7528\u7684\u662f\u670d\u52a1\u5668\u4e0d\u662f\u96c6\u7fa4\uff0c\u6240\u4ee5\u662f#<\/p>\n

--overlap<\/b>=100000 \u7247\u6bb5\u4e4b\u95f4\u7684\u8986\u76d6\u533a\u5927\u5c0f<\/p>\n

--chunksize<\/b>=10000000 \u62c6\u5206\u7684\u7247\u6bb5\u5927\u5c0f<\/p>\n

--outputdir<\/b>=.\/augDir \u8f93\u51fa\u6587\u4ef6\u5939<\/p>\n

--joblist<\/b>=jobs.lst \u547d\u4ee4\u5217\u8868<\/p>\n

--jobprefix<\/b>=augSplit_ \u8f93\u51fa\u7684\u6587\u4ef6\u524d\u7f00<\/p>\n

--command<\/b> \u5177\u4f53\u7684Augustus\u547d\u4ee4<\/p>\n

# \u8f93\u51fa\u7ed3\u679c<\/p>\n

augSplit_X<\/b>\uff1a\u6bcf\u4e2a\u5e76\u884c\u4efb\u52a1\u7684\u547d\u4ee4<\/p>\n

jobs.lst<\/b>\uff1a\u6574\u5408\u6bcf\u4e2a\u5e76\u884c\u4efb\u52a1\u6587\u4ef6\u7684\u5217\u8868\u6587\u4ef6<\/p>\n

 <\/p>\n

# \u8fd0\u884c\u5e76\u884cAugustus\u7a0b\u5e8f<\/p>\n

parallel -j 8 \"bash .\/{}\" < jobs.lst<\/p>\n

 <\/p>\n

#\u5408\u5e76\u5e76\u884c\u8fd0\u884c\u7684\u7ed3\u679c<\/p>\n

cat jobs.lst | xargs cat | sed -n 's\/^.*--outfile=\\(\\S*\\)\\s.*$\/\\1\/p' | xargs cat > augustus_concat.gtf<\/p>\n

singularity exec ..\/..\/container\/GENETools202309.sif join_aug_pred.pl < augustus_concat.gtf > augustus_combine.gtf<\/p>\n

# \u8f93\u51fa\u7ed3\u679c<\/p>\n

augustus_combine.gtf<\/strong>\uff1aAugustus\u7684\u8fd0\u884c\u7ed3\u679c\uff0c\u4e5f\u662fEVM\u7684\u8f93\u5165\u7684\u4ece\u5934\u9884\u6d4b\u7684\u7ed3\u679c<\/p>\n

 <\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

2.4 EVM\u8bc1\u636e\u6574\u5408<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

\u9884\u6d4b\u7ed3\u679c\u6587\u4ef6\u683c\u5f0f\u8c03\u6574\uff08\u53ea\u9700\u8981\u8c03\u6574Augustus\u548cminiprot\u7684\uff0cPASA\u4e0d\u9700\u8981\u8c03\u6574\uff09<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

# augustus\u7ed3\u679c\u8c03\u6574<\/p>\n

perl \/opt\/EVidenceModeler\/EvmUtils\/misc\/augustus_GTF_to_EVM_GFF3.pl augustus_combine.gtf > augustuts.gff3<\/p>\n

 <\/p>\n

# miniprot\u7ed3\u679c\u8c03\u6574<\/p>\n

python \/opt\/EVidenceModeler\/EvmUtils\/misc\/miniprot_GFF_2_EVM_alignment_GFF3.py ..\/04.miniprot\/miniprot.gff > miniprot.gff3<\/p>\n

 <\/p>\n

# \u5408\u5e76\u4ece\u5934\u9884\u6d4b\u7ed3\u679c\u6587\u4ef6\uff08PASA\u751f\u6210\u7684\u7ed3\u679c\u6587\u4ef6\u7136\u540e\u901a\u8fc7Transdecoder\u9884\u6d4b\u7684\u548cAugustus\u4ece\u5934\u9884\u6d4b\u7684\uff09<\/p>\n

cat augustuts.gff3 pasa_transdecoder.gff3 > evm.gene_predictions.gff3<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

\u8fd0\u884cEVM<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

EVidenceModeler --CPU 10 --sample_id Bra --genome genome.fasta --weights evm_weights.txt --gene_predictions evm.gene_predictions.gff3 --protein_alignments evm.protein_alignments.gff3 --transcript_alignments evm.transcript_alignments.gff3 --repeats ..\/..\/P1.RepeatAnno\/rmout_combine\/genome.out.gff --segmentSize 500000 --overlapSize 50000<\/p>\n

# \u53c2\u6570<\/p>\n

--CPU<\/b> \u8fd0\u884c\u7684\u7ebf\u7a0b\u6570<\/p>\n

--sample_id<\/strong> \u8f93\u51fa\u6587\u4ef6\u524d\u7f00<\/p>\n

--genome<\/strong> \u57fa\u56e0\u7ec4\u6587\u4ef6<\/p>\n

--weights<\/strong> \u6743\u91cd\u6587\u4ef6<\/p>\n

--gene_predictions<\/strong> \u4ece\u5934\u9884\u6d4b\u7ed3\u679c\u6587\u4ef6<\/p>\n

--protein_alignments<\/strong> \u86cb\u767d\u9884\u6d4b\u7ed3\u679c\u6587\u4ef6<\/p>\n

--transcript_alignments<\/strong> \u8f6c\u5f55\u7ec4\u9884\u6d4b\u7ed3\u679c\u6587\u4ef6<\/p>\n

--repeats<\/strong> \u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\u7ed3\u679c\u7684gff\u6587\u4ef6<\/p>\n

--segmentSize<\/strong> \u7247\u6bb5\u5927\u5c0f<\/p>\n

--overlapSize<\/strong> \u4e24\u4e2a\u8fde\u7eed\u7247\u6bb5\u7684\u91cd\u590d\u533a\u57df\u5927\u5c0f<\/p>\n

# \u8f93\u51fa\u7ed3\u679c<\/p>\n

.EVM.pep\uff1a<\/strong>\u8bc1\u636e\u6574\u5408\u540e\u9884\u6d4b\u7684pep\u6587\u4ef6<\/p>\n

.EVM.cds\uff1a<\/strong>\u8bc1\u636e\u6574\u5408\u540e\u9884\u6d4b\u7684cds\u6587\u4ef6<\/p>\n

.EVM.gff3\uff1a<\/strong>\u8bc1\u636e\u6574\u5408\u540e\u9884\u6d4b\u7684gff3\u683c\u5f0f\u6ce8\u91ca\u6587\u4ef6<\/p>\n

.EVM.bed:<\/strong>\u8bc1\u636e\u6574\u5408\u540e\u9884\u6d4b\u7684bed\u6587\u4ef6<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

\u51c6\u5907EVM\u7684\u6743\u91cd\u6587\u4ef6<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

# \u7b2c\u4e00\u5217\u672a\u8bc1\u636e\u540d \u7b2c\u4e8c\u5217\u662f\u6bcf\u4e2a\u9884\u6d4b\u7ed3\u679c\u7684\u7b2c\u4e09\u5217 \u7b2c\u4e09\u5217\u7684\u6bcf\u4e2a\u9884\u6d4b\u7ed3\u679c\u7684\u6743\u91cd<\/p>\n

PROTEIN miniprot_protAln 2 # \u86cb\u767d\u9884\u6d4b\u7ed3\u679c
TRANSCRIPT assembler-Bra-pasa.sqlite 10 # \u8f6c\u5f55\u7ec4\u9884\u6d4b\u7ed3\u679c
ABINITIO_PREDICTION Augustus 1 # \u4ece\u5934\u9884\u6d4b\u7ed3\u679c
OTHER_PREDICTION transdecoder 5 # \u5176\u4ed6\u9884\u6d4b\u7ed3\u679c<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

2.5 \u6ce8\u91ca\u6587\u4ef6\u4e2d\u6dfb\u52a0UTR\u548c\u53ef\u53d8\u526a\u5207<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

# \u68c0\u67e5\u6ce8\u91ca\u6587\u4ef6\u7684\u683c\u5f0f<\/p>\n

pasa_gff3_validator.pl Bra.EVM.gff3<\/p>\n

# \u52a0\u8f7dgff3\u6587\u4ef6\u5230\u6570\u636e\u5e93<\/p>\n

Load_Current_Gene_Annotations.dbi -c alignAssembly.config -g genome.fasta -P Bra.EVM.gff3<\/span><\/p>\n

# \u66f4\u65b0gff3\u6587\u4ef6<\/p>\n

Launch_PASA_pipeline.pl --CPU 10 -c annotCompare.config -A -g genome.fasta -t transcript.fasta<\/p>\n

# \u7b80\u5316gff3\u6587\u4ef6<\/p>\n

awk '$1 !~ \/^#\/' Bra-pasa.new.sqlite.gene_structures_post_PASA_updates.*.gff3 > Bra.EVM.update.gff3<\/p>\n

# \u63d0\u53d6PEP\u548cCDS<\/p>\n

gff3_file_to_proteins.pl Bra.EVM.update.gff3 genome.fasta prot > Bra.EVM.update.pep.fasta<\/p>\n

gff3_file_to_proteins.pl Bra.EVM.update.gff3 genome.fasta CDS > Bra.EVM.update.cds.fasta<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

\u66f4\u6539\u914d\u7f6e\u6587\u4ef6annotCompare.config<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

## templated variables to be replaced exist as <__var_name__><\/p>\n

# database settings
DATABASE=<__DATABASE__> # \u66f4\u6539\u4e3a\u4e4b\u524d\u6784\u5efa\u7684\u6570\u636e\u5e93\u540d\u79f0<\/strong><\/span><\/p>\n

#######################################################
# Parameters to specify to specific scripts in pipeline
# create a key = \"script_name\" + \":\" + \"parameter\"
# assign a value as done above.<\/p>\n

#script cDNA_annotation_comparer.dbi
cDNA_annotation_comparer.dbi:--MIN_PERCENT_OVERLAP=<__MIN_PERCENT_OVERLAP__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_PROT_CODING=<__MIN_PERCENT_PROT_CODING__>
cDNA_annotation_comparer.dbi:--MIN_PERID_PROT_COMPARE=<__MIN_PERID_PROT_COMPARE__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_LENGTH_FL_COMPARE=<__MIN_PERCENT_LENGTH_FL_COMPARE__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_LENGTH_NONFL_COMPARE=<__MIN_PERCENT_LENGTH_NONFL_COMPARE__>
cDNA_annotation_comparer.dbi:--MIN_FL_ORF_SIZE=<__MIN_FL_ORF_SIZE__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_ALIGN_LENGTH=<__MIN_PERCENT_ALIGN_LENGTH__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_OVERLAP_GENE_REPLACE=<__MIN_PERCENT_OVERLAP_GENE_REPLACE__>
cDNA_annotation_comparer.dbi:--STOMP_HIGH_PERCENTAGE_OVERLAPPING_GENE=<__STOMP_HIGH_PERCENTAGE_OVERLAPPING_GENE__>
cDNA_annotation_comparer.dbi:--TRUST_FL_STATUS=<__TRUST_FL_STATUS__>
cDNA_annotation_comparer.dbi:--MAX_UTR_EXONS=<__MAX_UTR_EXONS__>
cDNA_annotation_comparer.dbi:--GENETIC_CODE=<__GENETIC_CODE__><\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

2.6 \u63d0\u53d6\u6700\u957f\u8f6c\u5f55\u7ec4<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t

### gff3\u8f6c\u6362\u6210\u6807\u51c6ensembl gtf\u683c\u5f0f<\/p>\n

gffread -T genome.gff3 > tmp.genome.gtf<\/p>\n

### \u68c0\u67e5gtf\u6587\u4ef6\u662f\u5426\u6709\u989d\u5916\";\",\u5982\u6709\u66ff\u6362\u6210\"-\"<\/p>\n

# awk -F \"\\t\" '$NF ~ \/\"\\S+;\\S*\"\/' tmp.genome.gtf |less<\/p>\n

# mv tmp.genome.gtf tmp.gtf <\/span><\/p>\n

# sed 's\/\\( \"\\S*\\);\\(\\S*\"\\)\/\\1-\\2\/g' tmp.gtf > tmp.genome.gtf<\/p>\n

# rm tmp.gtf<\/p>\n

### \u8f6c\u6362\u6210\u6807\u51c6ensembl\u683c\u5f0f<\/p>\n

gtftk convert_ensembl -i tmp.genome.gtf > genome.gtf<\/p>\n

## \u7edf\u8ba1<\/span><\/p>\n

gtftk count -i genome.gtf > genome.gtf.count<\/span><\/p>\n

## \u63d0\u53d6\u7f16\u7801\u57fa\u56e0gtf\u5e76\u7edf\u8ba1<\/span><\/p>\n

gtftk select_by_key -k feature -v CDS -i genome.gtf | gtftk tabulate -k transcript_id,gene_id --unique --no-header > coding_mapid.txt<\/span><\/p>\n

perl ..\/script\/gtf_extract.pl genome.gtf coding_mapid.txt > genes_coding.gtf<\/span><\/p>\n

gtftk count -i genes_coding.gtf > genes_coding.gtf.count<\/p>\n

## \u7b5b\u9009\u6700\u957f\u8f6c\u5f55\u672c<\/span><\/p>\n

gtftk short_long -g -l -i genes_coding.gtf > genes_longest.gtf<\/span><\/p>\n

gtftk count -i genes_longest.gtf > genes_longest.gtf.count<\/span><\/p>\n

gffread -x genes_longest.cds.fasta -y genes_longest.pep.fasta -g genome.fasta genes_longest.gtf<\/span><\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

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