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statonlab / alternative_splicing_project

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Peach, chilling test #1

Closed RaymondS1 closed 4 years ago

RaymondS1 commented 4 years ago

Focusing on T3 and D7

RaymondS1 commented 4 years ago

Trimming 

for f1 in /staton/projects/alternative_splicing/peach/raw_reads/FastqGZ/*_R1_001.fastq
do
 f2=`sed 's/_R1/_R2/' <(echo $f1)`
 BASE1=$( basename $f1 | sed 's/.fastq*//g')
 BASE2=$( basename $f2 | sed 's/.fastq*//g')
 echo "f1 $f1"
 echo "f2 $f2"
 echo "BASE1 $BASE1"
 echo "BASE2 $BASE2"

 module load java/jdk8u181

 java -jar /staton/software/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 $f1 $f2 $BASE1.paired.trim.fastq $BASE1.unpaired.trim.fastq $BASE2.paired.trim.fastq $BASE2.unpaired.trim.fastq ILLUMINACLIP:/staton/software/Trimmomatic-0.38/adapters/all.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
done
RaymondS1 commented 4 years ago

HISAT

/staton/software/hisat2-2.1.0/hisat2 -p 8 --dta -x /staton/projects/alternative_splicing/peach/raw_reads/Prunus_persica_v2.0.a1_scaffolds.fasta -1
/staton/projects/alternative_splicing/peach/skewer/D7-1_CCGTCC_L007_R1_001.fastq-trimmed-pair1.fastq -2 /staton/projects/alternative_splicing/peach/skewer/D7-1_CCGTCC_L007_R1_001.fastq-trimmed-pair2.fastq -S ERR188044_chrX.sam$
RaymondS1 commented 4 years ago

HISAT2

for f1 in /staton/projects/alternative_splicing/peach/skewer/*-pair1.fastq
do
    f2=$(echo $f1 | sed 's/pair1/pair2/g')
    prefix=$( basename $f1 | sed 's/-pair1.fastq//g')
    echo "f1 $f1"
    echo "f2 $f2"
    echo "base $prefix"
    /staton/software/hisat2-2.1.0/hisat2 \
    -p 8 \
    -x /staton/projects/alternative_splicing/peach/HISAT \
    --dta \
    -1 $f1 \
    -2 $f2 \
    -S ./4_AS_HISAT/$prefix.sam \
    >& ./4_AS_HISAT/$prefix.output
done
RaymondS1 commented 4 years ago

SAM to BAM 

for SAMPLE in *sam
do
    prefix=$( basename $SAMPLE | sed 's/-trimmed.sam//g')
    echo "sam $SAMPLE"
    echo "sample $prefix"
    samtools sort \
    -@ 8 \
    -o sorted_bam/$prefix.bam \
    $SAMPLE
done
RaymondS1 commented 4 years ago

StringTie

for file in /staton/projects/alternative_splicing/peach/HISAT/4_AS_HISAT/sorted_bam/*.bam
do
prefix=$( basename $file | sed 's/.chr1.bam//g')
echo "sample $prefix"

/staton/software/stringtie-2.0.6.Linux_x86_64/stringtie \
-p 8 \
-G /staton/projects/alternative_splicing/peach/HISAT/Prunus_persica_v2.0.a1.gene.gtf \
-o StringTie/$prefix.chr1.gtf \
-l $prefix \
$file
done
RaymondS1 commented 4 years ago 
staton/software/stringtie-2.0.6.Linux_x86_64/stringtie --merge -p 8 -G /staton/projects/alternative_splicing/peach/HISAT/Prunus_persica_v2.0.a1.gene.gtf -o stringtie_merged.gtf mergelist.txt
RaymondS1 commented 4 years ago

Count Tables 

for file in /staton/projects/alternative_splicing/peach/HISAT/4_AS_HISAT/sorted_bam/*.bam
do
prefix=$( basename $file | sed 's/.chr1.bam//g')
echo "sample $prefix"

/staton/software/stringtie-2.0.6.Linux_x86_64/stringtie -e -B -p 8 -G /staton/projects/alternative_splicing/peach/StringTie/StringTie/stringtie_merged.gtf -o ./$prefix.count.gtf $file
done
RaymondS1 commented 4 years ago 
suppa.py generateEvents -i stringtie_merged.gtf -o events/T3-1/T3-1 -f ioe -e SE SS MX RI FL
RaymondS1 commented 4 years ago 
/staton/software/STAR-2.6.1a/bin/Linux_x86_64/STAR \
 --runMode genomeGenerate \
 --genomeDir /staton/projects/alternative_splicing/peach_STAR_test/raw_reads \
 --genomeFastaFiles /staton/projects/alternative_splicing/peach_STAR_test/raw_reads/Prunus_persica_v2.0.a1_scaffolds.fasta \
 --sjdbGTFfile /staton/projects/alternative_splicing/peach_STAR_test/raw_reads/Prunus_persica_v2.0.a1.gene.gff3 \
 --sjdbGTFtagExonParentTranscript Parent \
 --sjdbGTFfeatureExon CDS \
 --sjdbOverhang 100 &
RaymondS1 commented 4 years ago 
for f in /staton/projects/alternative_splicing/peach_STAR_test/skewer/*.log
do
 BASE=$( basename $f | sed 's/.log*//g')
 echo "BASE $BASE"

 /staton/software/STAR-2.6.1a/STAR \
  --genomeDir /staton/projects/alternative_splicing/peach_STAR_test/star/indexing/genomeDir \
  --readFilesIn /staton/projects/alternative_splicing/peach_STAR_test/skewer/$BASE-pair1.fastq /staton/projects/alternative_splicing/peach_STAR_test/skewer/$BASE-pair2.fastq \
  --outSAMtype BAM SortedByCoordinate \
  --outFileNamePrefix $BASE. &

done
RaymondS1 commented 4 years ago

StringTie

for file in /staton/projects/alternative_splicing/peach_STAR_test/star/alignment/*.bam
do
prefix=$( basename $file | sed 's/.chr1.bam//g')
echo "sample $prefix"

/staton/software/stringtie-2.0.6.Linux_x86_64/stringtie \
-p 8 \
-G /staton/projects/alternative_splicing/peach_STAR_test/raw_reads/Prunus_persica_v2.0.a1.gene.gtf \
-o StringTie/$prefix.chr1.gtf \
-l $prefix \
$file
done
RaymondS1 commented 4 years ago 
staton/software/stringtie-2.0.6.Linux_x86_64/stringtie --merge -p 8 -G /staton/projects/alternative_splicing/peach_STAR_test/raw_reads/Prunus_persica_v2.0.a1.gene.gtf -o stringtie_merged.gtf mergelist.txt
RaymondS1 commented 4 years ago 
for file in /staton/projects/alternative_splicing/peach_STAR_test/star/alignment/*.bam
do
prefix=$( basename $file | sed 's/.chr1.bam//g')
echo "sample $prefix"

/staton/software/stringtie-2.0.6.Linux_x86_64/stringtie -e -B -p 8 -G /staton/projects/alternative_splicing/peach_STAR_test/star/StringTie/StringTie/stringtie_merged.gtf -o 6_AS_count/$prefix.count.gtf $file
done