Web17 feb. 2015 · 1 I used this code below to install Trimmomatic: java -jar SE [-threads ] [-phred33 -phred64] [-trimlog ] ... I got a syntax error saying: -bash: syntax error near unexpected token `<' I appreciate it your help! terminal Share Improve this question Follow edited Feb 17, 2015 at 5:13 asked Feb 17, 2015 at 5:08 ocean 55 1 10 1 Webbuild_index: Build index for mapping using Salmon get_fastq: Download fastq files get_metadata: Download metadata from GEO and SRA get_srr: Download SRA run files …
Quality Control – NGS Analysis
Web17 aug. 2024 · Trimmomatic with Slurm DnA lab short read seq workshop 2024 460 views 9 months ago Module 18: Assembly Metrics w/ QUAST Hubbard Center for Genome Studies (HCGS) … WebTrimmomatic uses a two-step approach to find matches between the adapters and reads. First, short sections of each adapter (maximum 16 bp) are tested in each … buy frozen tickets perth
Using trimmomatic on multiple paired-end read files
WebThe first step is to gather your reference sequences of the organisms/sequences you do not want in your sample. Once you have all your contaminant sequences, put them all in a one file and index it with bowtie2. Note: Indexing with bowtie2 is only a requirement for the KneadData software. Web12 jun. 2024 · Running Trimmomatic Now we will run Trimmomatic on our data. To begin, navigate to your untrimmed_fastq data directory: $ cd /pool/genomics/username/dc_workshop/data/untrimmed_fastq We are going to run Trimmomatic on one of our single-end samples. Web1. Depending on the cluster management tool, you might have received e-mails when the "job" begins and ends. If so, you can check the "Exit status" of the job. For … buy frozen steaks online