Biostar

847 results • Page 1 of 17

Hello I am using Bash shell in windows and have installed Trimmomatic using sudo apt install trimmomatic Reading package lists... Done Building dependency tree Reading state information...Done trimmomatic is already the newest version (0.39+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 100 not upgraded. But when...I try to run commands it comes with error mo…

Trimmomatic NGS WGS

updated 2.3 years ago • ahmer

say what is wrong with me code, please. Thank you so much. java -jar /truba/home/sbuyukkilic/trimmomatic/Trimmomatic-0.39/trimmomatic-0.39.jar PE /truba/home/sbuyukkilic/fastqc_tool/sehriban SRR11192680_1.fastq.gz

Trimmomatic RNA-seq

updated 15 months ago • sehriban.buyukkilic

for the next stage (alignment), and should I make all the marks in the image green, and how do I use trimmomatic to get good results? I use this bash script ``` #!/bin/bash SECONDS=0 cd /home/tc/Project/Reads # run trimmomatic to trim reads...with poor quality java -jar /usr/share/java/trimmomatic-0.39.jar SE -threads 4 /home/tc/Project/Reads/ERR1880946.fastq.gz /home/tc/Project/trimm/ERR18…

Trimmomatic RNA quality-check

updated 15 months ago • Monia

Hello, everyone, I am trying to trim sequences from RNA seq data with Trimmomatic. For reference, I am using a Mac, and I have trimmomatic-0.39.jar in the trimmomatic folder in the Applications...working directory in the terminal. I am putting in the following code. java -jar Applications/Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 3 -phred33 raw_data/CON1/CON1_1.fq.gz raw_data/CON1/C…

trimmomatic

updated 22 months ago • Patricia

hi i have installed trimmomatic 0.36 on ubuntu 14.04 the following is the command i use : trimmomatic PE -threads 4 -phred33 DRR001913_1.fastq...unpaired_DRR001913_2.fastq AVGQUAL:20 SLIDINGWINDOW:4:15 MINLEN:50 error : trimmomatic: command not found for installation i have used the following commands : downloaded from this link : www.usadellab.org...cms/index.php?page=trimmomatic …

software error

updated 6.7 years ago • sanariyaz21

hi everyone, Is anyone can help me with trimmomatic problem?* I'm trying to run it but it's giving error like that: -bash-4.2$ java -jar /truba/home/sbuyukkilic/trimmomatic...Trimmomatic-0.39/trimmomatic-0.39.jar PE SRR12182130_1_fastqc.zip SRR12182130_1_fastqc.zip SRR12182130_1_paired_fastqc.zip

Trimmomatic rnaseq

updated 17 months ago • sehriban.buyukkilic

I've got a sra file in fastq format and I need to run single end Trimmomatic on the file. I've downloaded Trimmomatic in a new environment using conda command conda create -n trimmomatic...trimmomatic the command I used for executing the function is : trimmomatic SE -threads 4 SRR12304924_1.fastq/SRR12304924.trimmed.fastq

SE Trimmomatic

updated 2.6 years ago • ponmalar1120

java -jar /apps/eb/Trimmomatic/0.39-Java-1.8.0_144/trimmomatic-0.39.jar PE -phred33 seq1_L2_1.fq.gz seq1_L2_2.fq.gz _L2_r1_paired_fq.gz

Trimmomatic

updated 2.4 years ago • ronny

I am trying to install this trimmomatic file on my remote server (linux): https://github.com/timflutre/trimmomatic Whenever I proceed with the install...error: cd src/; javac -classpath ".:../lib/jbzip2-0.9.jar" -d ../classes org/usadellab/ trimmomatic/Trimmo…

trimmomatic makefile

updated 3.6 years ago • robbenstijn

and I'm trying to do trimming in RNA-Seq data on Ubuntu. -I'm using Windows- I downloaded Trimmomatic, and check by: ls Trimmomatic-0.39 Results; **LICENSE adapters trimmomatic-0.39.ja** But when I run this: trimmomatic...ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 It gives error: **trimmomatic: command not found** Can you help me

ubuntu trimmomatic RNA-Seq linux

updated 11 weeks ago • n_navy

to analysise my RNA seq data and now I am in the step of adaptor removal. I am trying to use trimmomatic and I loaded the module using command: **module load trimmomatic** Then I used the command to trim the adaptors: **java...jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz...PE.fa:2:30:10 LEADING:3 TRAILING…

RNA-Seq Trimmomatic jarfile

updated 6.7 years ago • Ambika

Hi friends, I was going to adapter trimming by trimmomatic then I did so but ``` [izadi@lbox161 ~]$ cd /usr/data/nfs6/izadi/Trimmomatic-0.33/ [izadi@lbox161 Trimmomatic-0.33]$ java -jar...trimmomatic-0.30.jar SE -phred33 SRR1944913.fastq output.fq ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW...4:15 MINLEN:36 Error: Unable to access jarfile trimmomatic-0.30.jar ``` Do you …

adapter trimmomatic

updated 20 months ago • Angel

Hi, all I have Double End fastq file and it needs trimming. So, I use trimmomatic software for this purpose.based on trimmomatic tutorial I write below code for my .fq.gz file: #!/bin/bash #PBS -N 04.trimmomatic...data=/histor/kang/guowei/lhr/trinity/ALL_DATA i=GT1-N2 adapter=/histor/kang/guowei/lhr/software/trimmomatic/Trimmomatic-0.39/adapters/TruSeq4-PE.fa trimmomatic=/histor/kang/guowe…

rnaseq

updated 2.6 years ago • liuhongran

Hello, I am attempting to use Trimmomatic to cut the adapters from my genome sequences. This is a crayfish genome sequenced with Illumina paired-end, short...with a coverage of ~ 150X. The poor quality sequences have already been trimmed prior to using trimmomatic, however, we still need to get rid of the adapters. I used the following script to run trimmomatic, modeled after...their example on t…

illumina genome adapters trimmomatic

updated 23 months ago • hpalk42

hello, I'm new here. I was using trimmomatic and I put this commands, trimmomatic PE -phred33 testadapt.1.fastq testadapt.2.fastq test_trim_paired.1.fq.gz...test_trim_paired.2.fq.gz test_trim_unpaired.2.fq.gz ILLUMINACLIP:/home/lab/Software/Trimmomatic-0.38/adapters/NexteraPE-PE.fa:2:30:10:4 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 but it reminds to me...trimmomatic: comman…

trimming software error

updated 5.4 years ago • SeaStar

1 I used the following codes: cd /mnt/gpfs2_4m/scratch/pba264/raw_reads module load ccs/conda/trimmomatic-0.39 for f in *fastq.gz; do output=/mnt/gpfs2_4m/scratch/pba264/Analysis/2-Trimmomatic/${f%.*}_trimmomatic.fastq.gz...log=/mnt/gpfs2_4m/scratch/pba264/Analysis/2-Trimmomatic/${f%.*}_trimmomatic.Log java -jar /mnt/gpfs2_4m/scratch/pba264/Applications/Trimmomatic/trimmomatic-0.39.jar...SE -t…

RNA-Seq

updated 3.8 years ago • pallob.barai

Hi All, I'm new to bioinformatics and currently working on some rna seq data. I'm using trimmomatic to remove adaptor contamination. I'm using the following script and I get the following message. It's been like...hour, how do I make sure its even working and not just stuck? ]$ java -jar /gscratch/stf/szahid/Trimmomatic-0.39/trimmomatic-0.39.jar PE -phred33 /gscratch/stf/szahid/VD03_R1_0…

RNA-Seq

updated 3.3 years ago • szahid

I want to install Trimmomatic tool. I downloaded software from below link and after unzip. I am trying to use make make install But these cammands...Please suggest how I can install this tool? http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip Thanks

RNA-Seq

updated 7.4 years ago • Bioinfonext

Hello everyone, I was doing Trimmomatic on paired fastq file, but this is giving an error. head SO_5494_LR_20_MS_01_S27_R2_001.fq @NS500223:167:H3T5HBGXY...While doing Trimmomatic it is giving this error, Exception in thread "main" java.lang.RuntimeException: Invalid FASTQ name line: -- at org.usadellab.trimmomatic.fastq.FastqParser.parseOne

NGS Trimmomatic Fastq

updated 12 months ago • Princy

hi all i have 21 sample from RNA-seq single end. i want trim that with trimmomatic. whether i can use command for. for f in *.fastq; do java -jar ~/sratoolkit.2.9.6-ubuntu64/apps/Trimmomatic-0.39/trimmomatic

rna-seq

updated 5.0 years ago • yaghoub.amraei

Hi all, I am really struggling with Trimmomatic these days and getting confused. I'm trying to run trimmomatic: java -jar trimmomatic-0.39.jar PE -threads 2 -phred33

Trimmomatic

updated 2.6 years ago • Xiaoyun

Hello, I performed trimmomatic for two pairs of my *sortmerna_1.fq.gz and *sortmerna_2.fq.gz files as follows: cd /scratch/fs/trimmomatic find...head -n 4 | while read FW_READ do read RV_READ FILEBASE=$(basename "${FW_READ%_1.fq.gz}") trimmomatic PE -threads 16 -phred64 "$FW_READ" "$RV_READ" \ "$FILEBASE-trimmomatic_1.fq.gz" "$FILEBASE-trimmomatic-unpaired_1.fq.g…

RNA-Seq Trimmomatic FastQC

updated 4.9 years ago • Farah

I recently ran Trimmomatic PE with the following thresholds: java -jar trimmomatic-0.36.jar PE f1 f2 f1_paired f1_unpaired f2_paired f2_unpaired...3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 I didn’t specify –phred, since I saw a message from Trimmomatic: >Quality encoding detected as phred33 So I think Trimmomatic (v 0.36) just uses –phred33 automatically since...Levels”, and “Kmer C…

RNA-Seq Trimmomatic FastQC

updated 4.7 years ago • tunl

Hello, I am using Trimmomatic to trim the adapter sequence from the raw small RNA data. For some reason after trimming I still find the adapter...trimmed sequence. Does anyone have any suggestion? This is the command I am using: java -jar trimmomatic SE -phred33 -threads 10 file_in file_out ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW...TGGAATTCTCGGGTG**CCAAGGAACTCCAG…

Trimmomatic small RNA

updated 5.4 years ago • S

I am using a M1 MacBook Pro and i'm not able to install trimmomatic successfullly. I tries using conda installer and ended up with an error. how to install trimmomatic from scratch

trimmomatic

updated 2.6 years ago • ponmalar1120

I am trying to run a sequencing file through Trimmomatic and each time I try to open the zipped file of Trimmomatic I encounter the error message "permission denied". This...I am trying to run a sequencing file through Trimmomatic and each time I try to open the zipped file of Trimmomatic I encounter the error message "permission denied". This is only my second day doing any sort of coding. I am …

Trimmomatic Error Linux Permission Denied

updated 6.0 years ago • boydmm6

Dear, I am running trimmomatic 0.35 to remove the adapters sequences from my Illumina data but I got the following error message Exception...SP_200_R2_unpaired_trimmo.fastq I used the following command ``` java \ -jar /home/bw14/doquispe/Trimmomatic-0.35/trimmomatic-0.35.jar \ PE \ -phred33 \ /home/bw14/doquispe/IlluminaSequences \ SP_200_R1.fastq SP_200_R2.fastq...SP_200_R2_unp…

next-gen Assembly

updated 21 months ago • dora.quispe

Hello, Which parameter in trimmomatic is most suitable for rectify per sequence GC content, sequence duplication level, and over represented sequences

fastqc trimm trimmomatic

updated 20 months ago • upasana

I have paired End fastq file and it needs trimming. So, I use trimmomatic software for this purpose. based on trimmomatic tutorial I write below code for my .fastq file: There is some error...how can I solve this problem? java -jar /mnt/d/trimomatic/Trimmomatic-0.39/Trimmomatic-0.39.jar PE -basein /mnt/d/raw/2023nudi/01.RawData/Nudivirus/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1_1.fq

trimmomatic whole-genome-sequencing linux

updated 9 months ago • 지영

Hi everyone, I am new to using trimmomatic, can anyone explain to me what the default settings are? This is the command I used: ``` Trinity \ --left R1V22_B9F8St_ACTTGA_L002_R1_001.fastq...right R1V22_B9F8St_ACTTGA_L002_R2_001.fastq \ --trimmomatic \ --max_memory 10G \ --CPU 16 \ --seqType fq \ --SS_lib_type RF \ --output /home/richardsonlab/AMMA_transcripts/trinity_out_dir2...no…

phred trinity rna-seq trimmomatic

updated 22 months ago • nikelle.petrillo

and keep getting errors **cannot execute binary file**. Is this a problem with my input files or TRIMMOMATIC itself ``` module load trimmomatic module load jdk/1.8.0.221 export TRIMMOMATIC=/opt/software/trimmomatic/0.39...trimmomatic-0.39.jar java -jar $TRIMMOMATIC PE \ -phred33 \ /scratch/marionr/Raw_Muscle_2021/41_L4_R1_001.fastq \ /scratch/marionr...LEADING:3 TRAILING:3 SLIDINGWINDOW:4:…

trimmomatic

updated 13 months ago • marion.ryan

I tried to run Trimmomatic 0.39 but ran into `Error: Invalid or corrupt jarfile /storage/home/user/tools/Trimmomatic-0.39/`. I went into the Trimmomatic...to the latest version. I configured my PATH for this tool `export PATH=/storage/home/user/tools/Trimmomatic-0.39/:$PATH` even tried `export PATH=/storage/home/user/tools/Trimmomatic-0.39/adapters:$PATH` and run trimmomatic...but still failed.…

trimmomatic ubuntu linux

updated 7 months ago • Emily

Hi, I am trying to run the Trimmomatic for multiple fastq.gz files. So, I am trying to run it in a loop at bash script. Please suggest ways to improve the...so the code has silly mistakes. for i in *_R1.fastq do java -jar /media/Data/apps/Trimmomatic-0.39/trimmomatic-0.39.jar PE -phred33 ${i}.1.fastq.gz ${i}.2.fastq.gz ${i}.trimmed_R1.fastq.gz ${i}.untrimmed_R1.fastq.gz..…

Trimmomatic fastq trimming

updated 2.1 years ago • Kumar

Hi all, I am a newbie here and I have some questions regarding to Nextera sequencing, Trimmomatic and subsequent downstream analysis. I appreciate your help and suggestions. Here is some of the background...Hi all, I am a newbie here and I have some questions regarding to Nextera sequencing, Trimmomatic and subsequent downstream analysis. I appreciate your help and suggestions. Here is some of …

next-gen sequencing Assembly

updated 7.2 years ago • h.l.wong

Hi all, I am trying to remove adapters and clean my RNA-seq.gz files using Trimmomatic, loaded on a Linux system (supercomputer server) Following the steps for Pair ends reads, explained in the manual...http://www.usadellab.org/cms/?page=trimmomatic) java -jar trimmomatic-0.39.jar PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz...ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:…

Illumina sequencing RNA-Seq Trimmomatic

updated 2.1 years ago • Seraph

to analyze my RNA seq data and now I am in the step of adapter removal. I am trying to use trimmomatic and I loaded the module using command: i downloaded the program to my home directory then unzipped it. But when...error. This is how I typed on my command line. java –jar/root/users/my home directory/apps/Trimmomatic-0.39/trimmomatic-0.39.jar PE -phred33 SRR3726664_1.fastq SRR3726664_2.…

rna-seq

updated 4.2 years ago • akashgari19

Illumina adpaters: https://ibb.co/ftDW6sK ![enter image description here][1] So I trimmed it using trimmomatic and following command (75 bases Single end reads): java -jar trimmomatic-0.39.jar SE input.fastq output.fastq...ILLUMINACLIP:TruSeq2-SE:2:30:10 and the same with TruSeq3 adapters: java -jar trimmomatic-0.39.jar SE input.fastq output.fastq ILLUMINACLIP:TruSeq3-SE:2:30:10 How…

RNA-Seq trimming

updated 4.8 years ago • Rimma

i didnt get the summary data either) curl -O http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip unzip Trimmomatic-0.36.zip #!/bin/bash for f1 in *_1.fastq.gz do withpath="${f1}" filename=${withpath...base="${filename%*_*.fastq.gz}" echo "${base}" java -jar ./Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 -trimlog trimmoatic.…

RNA-Seq trimmomatic

updated 6.5 years ago • kiddodoraemon

Hi Looking at this image, do I have to perform trimmomatic for this multiqc data or not. And if yes, what should be value for parameter like MINLEN.. ![multiqc][1] ![m2][2] [1]: /media/images

trimmomatic multiqc sra

updated 13 months ago • Nelo

I am using trimmomatic for quality trimming of fastq files for my project. im usig default values for paired end reads that trim the...I am using trimmomatic for quality trimming of fastq files for my project. im usig default values for paired end reads that trim the sequences...value for paired and single reads??? the command line im using is given below: java -jar trimmomatic-0.36.jar PE…

next-gen

updated 4.1 years ago • blooming.daisy333

try to defer from using any jargon so I can understand your points easier. Thank you. I am using Trimmomatic-0.36 and also undertaking this command on a remote server, rather than my local drive. The command line I have...recently used is the following: java -jar $trimmomatic PE -phred33 /home/will/240_CTTGTA_L004_R1_001.fastq.gz /home/will/C240_CTTGTA_L004_R2_001.fastq.gz C240_CTTGTA_L004_…

Directory Trimmomatic ILLUMINACLIP

updated 3.1 years ago • willbrown1999

Hi, what adapter file do I need to use to run Trimmomatic on miRNA-seq data generated on an Illumina Next-seq? I don't see any miRNA adapter file provided with Trimmomatic

miRNA-seq adapter Trimmomatic

updated 5.8 years ago • inah

I have SRR15324080 file. This file is paired end sequencing. How do I give it to Galaxy Server, Trimmomatic flexible read trimming tool for Illumina NGS data tool

to Trimmomatic input

updated 2.7 years ago • m.esmaeilpour

Hi Biostars, I need to cut only adapters from my data using trimmomatic. I used the following command: java -jar /home/ghovhannisyan/Softs/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads

trimmomatic RNA-Seq

updated 5.7 years ago • grant.hovhannisyan

some read data but i'm getting an error message. This is my input java -jar /home/yun/Downloads/Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 2 -phred33 ly1_1.fq ly1_2.fq \ly1_paired_1.trim.fq.gz ly1_unpaired_1.trim.fq.gz

Trimmomatic

updated 12 months ago • Xiaoyun

I want to run trimmomatic with Trinity, but there's some error that I can't solve. “ILLUMINACLIP:/tempwork173/r09b45015/anaconda3/envs/rnaseq...share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:20 TRAILING:3 MINLEN:25” **Error, do not understand options

Trinity

updated 2.3 years ago • YATING

reads directly from the input params, so I know they exist, and have given them full paths, however, Trimmomatic still has a file not found exception being thrown. I'm not sure what else to try. Any help is appreciated. Thank you...Error executing process > 'trimSR (Trimmomatic on Short Reads)' Caused by: Process `trimSR (Trimmomatic on Short Reads)` terminated with an error exit statu…

trimmomatic

updated 12 months ago • awhale01

Hi everyone, I was trying to do the adaptor trimming for my paired end RNA-seq data and I am using trimmomatic. I gave the following commands: *java -jar trimmomatic-0.35.jar PE -phred33 SL264821_1.fastq.gz SL264821_2.fastq.gz...3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36* but it gives me the error **Unable to access jarfile trimmomatic-0.35** . Could you please help me with this because I am …

RNA-Seq Trimmomatic Paired end reads

updated 5.6 years ago • Ambika

According to fastqc report, fastq files contain adapter sequences that I need to remove so I used Trimmomatic. But Trimmomatic produced 4 files:**R1 paired** , **R2 paired** , **R1 unpaired** and **R2 unpaired**. Which of these 2 files I can use

alignment Galaxy

updated 12 months ago • anasjamshed

Hi everyone, I just got my results after I ran trimmomatic command. I had 50bp paired end reads for which I ran the following command **java -jar /opt/asn/apps/trimmomatic_0.35...Trimmomatic-0.35/trimmomatic-0.35.jar PE -phred33 SL264821_1.fastq.gz SL264821_2.fastq.gz SL264821_1_paired.fastq.gz

RNA-Seq Trimmomatic Result

updated 6.7 years ago • Ambika

847 results • Page 1 of 17

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