Skip to content

TutorialInteractomeSeqCLI_Eucaryotic.md

Latest commit

 

History

History
468 lines (261 loc) · 11.9 KB

TutorialInteractomeSeqCLI_Eucaryotic.md

File metadata and controls

468 lines (261 loc) · 11.9 KB

1) Data download

Remenber to activate conda interactomeseq env

conda activate interactomeseq
(interactomeseq) 

pwd -P
mkdir -p InteractomeSeqCLIEukaryotic
(interactomeseq) 

cd InteractomeSeqCLIEukaryotic
(interactomeseq) 

WorkingDir=$(pwd)
(interactomeseq) 

processor=10
(interactomeseq) 

echo $WorkingDir
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic
(interactomeseq) 

time wget http://interactomeseq.ba.itb.cnr.it/services/InteractomeSeq/Eukaryote.Uploading/Eukaryote_RnaBindProt.zip -P $WorkingDir
--2020-04-10 14:15:35--  http://interactomeseq.ba.itb.cnr.it/services/InteractomeSeq/Eukaryote.Uploading/Eukaryote_RnaBindProt.zip
Risoluzione di interactomeseq.ba.itb.cnr.it (interactomeseq.ba.itb.cnr.it)... 150.145.82.8
Connessione a interactomeseq.ba.itb.cnr.it (interactomeseq.ba.itb.cnr.it)|150.145.82.8|:80... connesso.
Richiesta HTTP inviata, in attesa di risposta... 200 OK
Lunghezza: non specificato [text/plain]
Salvataggio in: "/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/Eukaryote_RnaBindProt.zip"

Eukaryote_RnaBindPr     [               <=>  ] 105,76M  6,03MB/s    in 17s     

2020-04-10 14:15:52 (6,36 MB/s) - "/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/Eukaryote_RnaBindProt.zip" salvato [110902666]


real	0m16,682s
user	0m0,092s
sys	0m0,428s
(interactomeseq) 

time wget interactomeseq.ba.itb.cnr.it/services/InteractomeSeq/Eukaryote.Uploading/Homo_sapiens.GRCh38.99.zip -P $WorkingDir
--2020-04-10 14:16:54--  http://interactomeseq.ba.itb.cnr.it/services/InteractomeSeq/Eukaryote.Uploading/Homo_sapiens.GRCh38.99.zip
Risoluzione di interactomeseq.ba.itb.cnr.it (interactomeseq.ba.itb.cnr.it)... 150.145.82.8
Connessione a interactomeseq.ba.itb.cnr.it (interactomeseq.ba.itb.cnr.it)|150.145.82.8|:80... connesso.
Richiesta HTTP inviata, in attesa di risposta... 200 OK
Lunghezza: non specificato [text/plain]
Salvataggio in: "/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/Homo_sapiens.GRCh38.99.zip"

Homo_sapiens.GRCh38     [     <=>            ]   1,90G  3,57MB/s    in 6m 46s  

2020-04-10 14:23:40 (4,81 MB/s) - "/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/Homo_sapiens.GRCh38.99.zip" salvato [2043656730]


real	6m45,648s
user	0m1,576s
sys	0m10,396s
(interactomeseq) 

cd $WorkingDir
ls 
mkdir -p rawdata
(interactomeseq) 

mkdir -p references
(interactomeseq) 

time unzip -d rawdata Eukaryote_RnaBindProt.zip
Archive:  Eukaryote_RnaBindProt.zip
  inflating: rawdata/Delta5Uchl1ssDNA.fastq.gz  
  inflating: rawdata/Delta5Uchl1tRNA.fastq.gz  
  inflating: rawdata/invSINEB2ssDNA.fastq.gz  
  inflating: rawdata/invSINEB2tRNA.fastq.gz  
  inflating: rawdata/NotSelected.fastq.gz  
  inflating: rawdata/Eukaryote_RnaBindProt_Tutorial.pdf  

real	0m0,834s
user	0m0,632s
sys	0m0,080s
(interactomeseq) 

time unzip -d references Homo_sapiens.GRCh38.99.zip
Archive:  Homo_sapiens.GRCh38.99.zip
  inflating: references/Homo_sapiens.GRCh38.99.bed  
  inflating: references/Homo_sapiens.GRCh38.99.cdna.all.fa  
  inflating: references/Homo_sapiens.GRCh38.99.sizes.genome  
  inflating: references/Homo_sapiens.GRCh38.99.chr.gtf  
  inflating: references/Homo_sapiens.GRCh38.99.idx  
  inflating: references/Homo_sapiens.GRCh38.99.sizes.transcriptome  

real	0m33,296s
user	0m30,424s
sys	0m2,856s
(interactomeseq) 

cd rawdata
(interactomeseq) 

time gunzip *.fastq.gz 
real	0m6,333s
user	0m5,548s
sys	0m0,776s
(interactomeseq) 

ls
Delta5Uchl1ssDNA.fastq  Eukaryote_RnaBindProt_Tutorial.pdf  invSINEB2tRNA.fastq
Delta5Uchl1tRNA.fastq   invSINEB2ssDNA.fastq                NotSelected.fastq
(interactomeseq) 

pwd
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/rawdata
(interactomeseq) 

RawData=$(pwd)
(interactomeseq) 

cd $WorkingDir
(interactomeseq) 

cd references
(interactomeseq) 

Reference=$(pwd)
(interactomeseq)

Now we are ready to start the analysis with InteractomeSeqCLI

cd $WorkingDir
(interactomeseq) 

git clone https://github.com/sinnamone/InteractomeSeq
Cloning into 'InteractomeSeq'...
remote: Enumerating objects: 61, done.�[K
remote: Counting objects: 100% (61/61), done.�[K
remote: Compressing objects: 100% (48/48), done.�[K
remote: Total 608 (delta 24), reused 41 (delta 13), pack-reused 547�[K
Ricezione degli oggetti: 100% (608/608), 304.66 KiB | 0 bytes/s, done.
Risoluzione dei delta: 100% (434/434), done.
(interactomeseq) 

samtools faidx  "$Reference"/Homo_sapiens.GRCh38.99.cdna.all.fa
(interactomeseq)

2) Mapping reads against reference Homo Sapiens genome

cd "$WorkingDir"
(interactomeseq) 

ls 
mkdir -p output
(interactomeseq) 

cd "$WorkingDir"/InteractomeSeq/PyinteraseqEukaryotic
(interactomeseq) 

time for i in NotSelected invSINEB2tRNA invSINEB2ssDNA Delta5Uchl1tRNA  Delta5Uchl1ssDNA; do python pyinteraseq_main_mapping.py --readforward "$RawData"/"$i".fastq --outputfolder  "$WorkingDir"/output/ --primer5forward GCAGCAAGCGGCGCGCATGC --primer3forward GCGCTTCGTCAT --fastasequence  "$Reference"/Homo_sapiens.GRCh38.99.cdna.all.fa --thread $processor --outputid "$i" --kallistoindex "$Reference"/Homo_sapiens.GRCh38.99.idx --genomesize "$Reference"/Homo_sapiens.GRCh38.99.sizes.genome --transcriptsize "$Reference"/Homo_sapiens.GRCh38.99.sizes.transcriptome --gtf "$Reference"/Homo_sapiens.GRCh38.99.chr.gtf ; done
real	11m51,442s
user	10m34,396s
sys	1m15,256s
(interactomeseq) 

ls "$WorkingDir"/output/*_mapping.*
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1ssDNA_mapping.bam
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1ssDNA_mapping.bam.bai
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1ssDNA_mapping.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1tRNA_mapping.bam
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1tRNA_mapping.bam.bai
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1tRNA_mapping.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2ssDNA_mapping.bam
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2ssDNA_mapping.bam.bai
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2ssDNA_mapping.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2tRNA_mapping.bam
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2tRNA_mapping.bam.bai
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2tRNA_mapping.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/NotSelected_mapping.bam
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/NotSelected_mapping.bam.bai
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/NotSelected_mapping.log
(interactomeseq)

3) Domain Definition

time for i in Delta5Uchl1ssDNA Delta5Uchl1tRNA invSINEB2ssDNA invSINEB2tRNA NotSelected ; do python pyinteraseq_main_domain_definition.py --mappingoutput "$WorkingDir"/output/"$i"_mapping.bam --outputfolder "$WorkingDir"/output/ --outputid "$i" --fastasequence "$Reference"/Homo_sapiens.GRCh38.99.cdna.all.fa --annotation "$Reference"/Homo_sapiens.GRCh38.99.bed --threshold 30 --genome "$Reference"/Homo_sapiens.GRCh38.99.sizes.transcriptome ; done 
sys:1: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
sys:1: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
sys:1: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
sys:1: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
sys:1: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.

real	13m30,204s
user	12m30,980s
sys	0m52,764s
(interactomeseq) 

ls "$WorkingDir"/output/*_definition.*
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1ssDNA_definition.txt
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1ssDNA_domain_definition.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1tRNA_definition.txt
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1tRNA_domain_definition.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2ssDNA_definition.txt
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2ssDNA_domain_definition.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2tRNA_definition.txt
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2tRNA_domain_definition.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/NotSelected_definition.txt
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/NotSelected_domain_definition.log
(interactomeseq)

Domain Enrichment

time python pyinteraseq_enrichment_eukaryotic.py --outputcontrol "$WorkingDir"/output/invSINEB2ssDNA_definition.txt  --outputarget "$WorkingDir"/output/invSINEB2tRNA_definition.txt --outputfolder "$WorkingDir"/output/ --outputid invSINEB2tRNAvsinvSINEB2ssDNA 
real	0m2,024s
user	0m1,804s
sys	0m0,472s
(interactomeseq) 

time python pyinteraseq_enrichment_eukaryotic.py --outputcontrol "$WorkingDir"/output/Delta5Uchl1ssDNA_definition.txt  --outputarget "$WorkingDir"/output/Delta5Uchl1tRNA_definition.txt --outputfolder "$WorkingDir"/output/ --outputid Delta5Uchl1tRNAvsDelta5Uchl1ssDNA 
real	0m2,418s
user	0m2,268s
sys	0m0,620s
(interactomeseq) 

ls "$WorkingDir"/output/*_intervals.*
ls "$WorkingDir"/output/*_enrichment.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1tRNAvsDelta5Uchl1ssDNA_common_intervals.txt
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1tRNAvsDelta5Uchl1ssDNA_unique_intervals.txt
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2tRNAvsinvSINEB2ssDNA_common_intervals.txt
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2tRNAvsinvSINEB2ssDNA_unique_intervals.txt
(interactomeseq) /home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/Delta5Uchl1tRNAvsDelta5Uchl1ssDNA_enrichment.log
/home/spuccio/InteractomSeqCLIEukaryotic/InteractomeSeqCLIEukaryotic/output/invSINEB2tRNAvsinvSINEB2ssDNA_enrichment.log
(interactomeseq) 

echo "Done"
Done
(interactomeseq)