Recover assembly results (only Trinity.fasta) generated by trinity from the shared location to your scratch directory :.Jobs = shows jobs running fg = foreground bf = background ctrl + z = send job to background ctrl + c = kill job in ground WARNING !: This job is expected to run 12 hours. Butterfly: resolves alternatively spliced and paralogous transcripts independently for each cluster (in parallel)Įnding up assembly and downloading assembly results.Chrysalis: Clusters overlapping Inchworm contigs, builds de Bruijn graphs for each cluster, partitions reads between clusters.Inchworm: Assembles initial contigs by “greedily” extending sequences with most abundant K-mers.Jellyfish: Extracts and counts K-mers (K=25) from reads.trinity.log.Īfter trimmomatic and reads normalisation, Three stages are done by Trinity While running you can examine steps tail -f.
You can use jobs to monitor jobs but if you logout the program does not keep running. That the terminal will return to the prompt right after you hit “Enter”. The script will start executing in the background (the & at the end), so log &Īll screen output (info messages and error messages, if any) will be saved in the file Trinity - seqType fq - max_memory 50 G - CPU 2 - trimmomatic - quality_trimming_params 'ILLUMINACLIP:/usr/local/Trimmomatic-0.33/adapters/TruSeq2-PE.fa:2:30:10 ILLUMINACLIP:/scratch/formationX/RAWDATA/adapt-125pbLib.txt:2:30:10 SLIDINGWINDOW:5:20 LEADING:5 TRAILING:5 MINLEN:25 HEADCROP:10' - normalize_by_read_set - samples_file samples. # Running Trinity with trimmomatic and normalisation # Trinity -seqType fq -max_memory 50G -CPU 2 -samples_file samples.txt -output. 5 module load bioinfo / Trimmomatic / 0.33 # changing PATH to current directory in samples file Module load bioinfo / samtools / 1.9 module load bioinfo / trinityrnaseq / 2.8. If you need launch it in a slurm cluster you can use this version containing SBATCH commands run_trinity.slurm or adapt it to SGE. This script is not sending in sbatch mode because it could be take time in this training. Observe run_trinity.sh script and adapt to your formation number.
Performing a de novo RNA-Seq assembly with trinity 2.1 Running Trinity with trimmomatic and reads normalisation Preparing assembly sample file and check parameters of trinity assembler Remove contaminations with SortMeRNA, riboPicker or DeconSeq.Ģ. Use PRINSEQ2 to detect Poly A/T tails and low complexity reads. To remove adaptors and primers you can use Trimmomatic. You need to observe sequences and check biases. Scp - r multiqc * nas : / home / formationX / # transfert results to your local machine by scp or filezilla Module load bioinfo / multiqc / 1.7 #launch Multiqc to create a report in html containing the whole of informations generated by FastQC
Use this tool to visualise results of quality. Multiqc is a modular tool to aggregate results from bioinformatics analyses across many samples into a single report. 1 # run fastqc in the whole of samplesįastqc - t 2 / scratch / formationX / RAWDATA /*. gzįastQC perform some simple quality control checks to ensure that the raw data looks good and there are no problems or biases in data which may affect how user can usefully use it. You should see 12 gzipped read files in a listing, the samples.txt file and the run_trinity.sh bash script. When the files transfer is finished, verify by listing the content of the current directory and the subdirectory RAWDATA with theĬommand ls -al.Scp - r nas : / data2 / formation / TP - trinity / SRA_SRS307298 / RAWDATA / / scratch / formationX / Copy the exercise files from the shared location to your scratch directory (it is essential that all.In the following, please replace X with your own user ID number in formationX.Ĭd / scratch mkdir formationX cd formationX Create your subdirectory in the scratch file system /scratch.Read this survival document containig basic commands to SLURM () srun - p supermem - mem 50 G - time 20 : 00 : 00 - cpus - per - task 2 - pty bash - i Prepare input files fr Opening an interactive bash session on the node25 (supermem partition) - srun -p partition -pty bash -i We will work on the i-Trop Cluster with a “supermem” node using SLURM scheduler. Connection to the i-Trop Cluster through ssh mode It is from two different origin (CENPK and Batch), with three biological replications for each In this session, we will analyze RNA-seq data from one sample of S. data : NCBI SRA database under accession number SRS307298 S.Going to the i-Trop cluster - ssh,srun,scpĭataset used in this practical comes from Performing a de novo RNA-Seq assembly with trinity Going to the i-Trop cluster - ssh,srun,scp Julie Orjuela-Bouniol - i-Trop platform (UMR BOREA / DIADE / IPME - IRD)Ĭhristine Tranchant Preambule : 0. Hands On Lab Exercises for RNASeq assembly
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