Hisat-Trinity-PASA等组学分析流程

本文介绍: 主要发表或收录生物信息学的教程，以及基于R的分析和可视化（包括数据分析，图形绘制等）；分享感兴趣的文献和学习资料!这里只是提供了各个分析流程的脚本，对于初学者来说是比较有好的。中提供了详细转录组上游分析的参数，对于初学者来说是比较友好的。

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详细教程请访问：
组学分析流程

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#!/bin/bash

genome=$1
index=${genome%.*}
rna_1_fq=`cat $2|grep 1P|sed ":a;N;s/n/,/g;ta"` #1.fq path list
rna_2_fq=`cat $2|grep 2P|sed ":a;N;s/n/,/g;ta"` #2.fq path list

#echo $index
hisat2-build -p 20 $genome $index

hisat2 -x $index 
           -1 $rna_1_fq
           -2 $rna_2_fq
           --threads 20 
           --min-intronlen 20 
           --max-intronlen 20000 
           --dta 
           --score-min L,0.0,-0.4 
           -S ${index}.sam


samtools sort -@ 20 
                  -o ${index}.sorted.bam 
                      -O BAM 
                ${index}.sam

#!/bin/bash

export PATH="$PATH:/usr_storage/jcf/.conda/envs/PASA"
source  /pub_storage2/new_PASA/.bashrc

#cat $Trinity_GG $Trinity_denovo &gt;transcripts.fasta #
transcripts_fasta="$1" # transcripts.fasta generated from merging fasta file of Trinity denovo and Trinity genome guided mode

#perl -e 'while(<>) { print "$1n" if />(S+)/ }' Trinity.fasta >tdn.accs #
denovo_transcript_id="$2" 
alignAssembly_config="$3"
genome="$4" #reference fasta file



seqclean $transcripts_fasta 
	     -v /pub_storage2/PASA/UniVec
		 

Launch_PASA_pipeline.pl -c $alignAssembly_config 
					    -C -R -T 
						-g $genome  
						-t $transcripts_fasta.clean 
						-u ${transcripts_fasta} 
						--ALIGNERS gmap,blat 
						--CPU 8  
						--TDN $denovo_transcript_id

#!/bin/bash

#conda activate trinity

export PATH="$PATH:/usr_storage/jcf/.conda/envs/trinity"

rna_1_fq="cat $1|sed ":a;N;s/n/,/g;ta"" #1.fq path list 
rna_2_fq="cat $2|sed ":a;N;s/n/,/g;ta"" #2.fq path list
bam="$3"  #sorted.bam from hisat
out=${bam%.*}


Trinity --left $rna_1_fq 
	    --right $rna_2_fq 
		--seqType fq  
		--max_memory 100G 
		--no_normalize_reads 
		--CPU 20 
		--bflyCalculateCPU  
		--output trinity_denovo_$out
		
Trinity --genome_guided_bam $bam  
		--genome_guided_max_intron 10000 
		--max_memory 100G 
		--no_normalize_reads 
		--CPU 20 
		--bflyCalculateCPU
		--output trinity_GG_$out

#!/bin/bash

export PATH="$PATH:/usr_storage/jcf/.conda/envs/BUSCO"
source /usr_storage/jcf/geta-user204/.bashrc


rna_1_fq="cat $1|sed ":a;N;s/n/,/g;ta"" #1.fq path list 
rna_2_fq="cat $2|sed ":a;N;s/n/,/g;ta"" #2.fq path list
genome="$3" #genome fasta file 
conf="$4" #small genome conf.txt of geta pipepline setting as default parameters
out=${genome%.*}
homo_pro="$5"

geta.pl 
	--RM_species Embryophyta
	--out_prefix `pwd`/$out 
	--config $conf 
	--cpu 20 
	--protein $homo_pro
	-genome $genome 
	-1 $rna_1_fq 
	-2 $rna_2_fq 
	--augustus_species $out

#!/bin/bash

export PATH="/usr_storage/xyf/jcf/genewise/EVM/EVidenceModeler-1.1.1/EvmUtils/:$PATH"

genome="$1" #genome fasta file 
augustus_gff3="$2" #gff3 generated from augutus 
genewise_gff3="$3" #gff3 generated from tblastn and genewise
pasa_align_gff3="$4" #gff3 generated from PASA 
repeat_gff3="$5" #repeat gff3 generated from repeatemasker
partition="$6" #partition path for evm



partition_EVM_inputs.pl 
		--genome $genome
		--gene_predictions $augustus_gff3 
		--protein_alignments $genewise_gff3 
		--transcript_alignments $pasa_align_gff3 
		--repeats $repeat_gff3 
		--segmentSize 5000000 
		--overlapSize 10000 
		--partition_listing $partition
		
write_EVM_commands.pl 
		--genome $genome 
		--gene_predictions $augustus_gff3 
		--protein_alignments $genewise_gff3 
		--transcript_alignments $pasa_align_gff3 
		--repeats $repeat_gff3 
		--output_file_name evm.out 
		--weights $weight >command.list
		
ParaFly -c command.list -CPU 32 

recombine_EVM_partial_outputs.pl 
		--partitions $partition 
		--output_file_name evm.out 
		
convert_EVM_outputs_to_GFF3.pl 
		--partitions $partition 
		--output_file_name evm.out 
		--genome  $genome 

cat */evm.out.gff3 >evm.out.gff3

#!/bin/bash


export PATH="$PATH:/usr_storage/jcf/.conda/envs/PASA "
source  /pub_storage2/new_PASA/.bashrc

genome="$1" #genome fasta file
annotation_conf="$2" #pasa annotation compare conf 
transcripts_fasta="$3" #transcripts_fasta file for PASA seqclean step
gff3="$4" #gff3 for PASA updata


Launch_PASA_pipeline.pl 
		-c $annotation_conf
		-A -T -L 
		-g $genome
		-t ${transcripts_fasta}.clean 
		-u $transcripts_fasta 
		--annots $gff3