Biostar

883 results • Page 2 of 18

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 23 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 6.6 years ago • Ambika

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 7.6 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 23 months ago • anasjamshed

Seq FASTQ files, but it's not working.. The parameters I'm using are: java -jar ~/Applications/Trimmomatic-0.39/trimmomatic-0.39.jar SE -phred33 shock02_RNASeq.fastq.gz trimmed_shock02.fastq.gz LEADING:3 TRAILING

Trimmomatic

updated 6 months ago • pinheirofabiano

Hi all, I am really struggling with Trimmomatic these days and the frustration level is rising (I have to meet a deadline). For multiple days Trimmomatic, on usegalaxy.org, has given me an error as soon as I apply the IlluminaClip: > Fatal error: Exit code 1 () Trimmomatic did not finish successfully It works like a charm when applying the options for quality trimming, head-crop etc...…

RNA-Seq software error sequence next-gen

updated 8.1 years ago • BioBing

simple of rnaseq analysis and I want to trim them before alignment. Can someone help me to provide trimmomatic code for analysis of all samples at once. Otherwise I have to run the same code for 20 times. Thank you for understanding

Multiple sample

updated 2.5 years ago • Ram

I've been using Trimmomatic by using LEADING, TRAILING and SLIDING WINDOW parameters. Recently we have seen that ILLUMINACLIP parameter...I've been using Trimmomatic by using LEADING, TRAILING and SLIDING WINDOW parameters. Recently we have seen that ILLUMINACLIP parameter is also being used mostly. Until we have seen this, we have been thinking that Trimmomatic is built to trim Illumina adapters…

RNA-Seq trimming trimmomatic illuminaclip

updated 6.1 years ago • Batu

Hi, I use Trimmomatic v0.35 and I notice the option `-validatePairs`: Usage: PE [-threads ] [-phred33|-phred64] [-trimlog ] [-quiet] [-validatePairs...in the manual. I want to filter away singletons from two paired fastq-files and I tried to run trimmomatic with this option and the two paired files as input, but it didn't work. Thanks, Jon

trimmomatic

updated 6.8 years ago • jon.brate

HOME/workdir/group" output_dir="$HOME/workdir/group/fqdata_trimmed" adap="$CONDA_PREFIX/share/trimmomatic-0.39-1/adapters" f1="$HOME/workdir/group/P4.R1.fq.gz" f2="$HOME/workdir/group/P4.R2.fq.gz" newf1="$HOME/workdir/group...mismatch_values=(1 2 3 4 5) for mismatch_value in "${mismatch_values[@]}" do trimmomatic PE -threads 1 -phred33 -trimlog trimLogFile -summary statsSummaryFile …

Trimmomatic adap

updated 23 months ago • eshrakaali_p

Hello, I am new to Bioinformatics, I have done Trimmomatic of my fastq sequences, I have 4 samples with 3 replicates each. now I have paired and unpaired reads. Do I need to...Hello, I am new to Bioinformatics, I have done Trimmomatic of my fastq sequences, I have 4 samples with 3 replicates each. now I have paired and unpaired reads. Do I need to merge

Trinty Trimmomatic merge paired

updated 3.6 years ago • Princy

hi every one recently I used trimmomatic for my fastq data but I can't find the output in the current directory where is the problem??? where are they???? my command...was: java -jar trimmomatic-0.39.jar PE ERR3301300_1.fastq ERR3301300_2.fastq ERR3301300_FP.fastq ERR3301300_FU.fastq ERR3301300_RP.fastq

RNA-Seq gene trimmomatic

updated 4.7 years ago • mo.ghasemi717

workdir/group" output_dir="$HOME/workdir/group/fqdata_trimmed" adap="$CONDA_PREFIX/share/trimmomatic-0.39-1/adapters" f1="$HOME/workdir/group/P4.R1.fq.gz" f2="$HOME/workdir/group/P4.R2.fq.gz" newf1="$HOME/workdir/group...mismatch_values=(1 2 3 4 5) for mismatch_value in "${mismatch_values[@]}" do trimmomatic PE -threads 1 -phred33 -trimlog trimLogFile -sum…

Trimmomatic adap

updated 23 months ago • eshrakaali_p

Trimmomatic can't seem to find my adapter files, and I've tried a lot of different pathways but nothing works. Any help is appreciated...thanks. Here's my code: ``` for file in ../../fqgz_trim_single/*R1_001.fastq.gz do trimmomatic SE -threads 1 -phred33 -trimlog $file ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15

Trimmomatic

updated 2.2 years ago • ng

Hi, I have Single 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: java -jar /home/ubuntu...CIRI_v2.0.6/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred64 sra_data_SRR1427482.fastq SRR1427482 LEADING=20 TRAILING=20 HEADCROP

RNA-Seq

updated 7.0 years ago • modarzi

Hi I m begening at bioinformatic ,i want use trimmomatic for trimming my data , i install trimmomatic by conda , and i use this command trimmomatic PE -phred33 ERR770964_1.fastq

software error

updated 5.9 years ago • haddadfatiha62

I am running trimmomatic using the following command: java -jar ~/tools/Trimmomatic-0.32/trimmomatic-0.32.jar PE R1_001.fastq R2_001.fastq

sequence next-gen-sequencing RNA-Seq

updated 3.2 years ago • xuanyuan

I am using trimmomatic for quality trimming of Paired reads. however, i am unable to get equal numbrer of reads in paired read files. Can...please help me out to resolve this issue. the command I am using is as follows: java -jar trimmomatic-0.36.jar -phred33 PE /path/to/dir/SRR9590_1.fastq /path/to/dir/SRR9590_2.fastq SRR9590_1P.fq SRR9590_1U.fq

sequencing

updated 7.0 years ago • blooming.daisy333

4] I next removed adapters and low quality bases using a sliding window of 4:30 using trimmomatic, but after trimming I only have 87% of my reads remaining. Could someone please explain why trimmomatic is removing...10% of my reads even though the quality of my raw sequences is pretty good? This is the command for trimmomatic: java -jar trimmomatic-0.39.jar PE -threads 32 -trimlog SF1-1-C…

RNA-Seq Trimmomatic Quality

updated 5.7 years ago • sneha108ss

Hi, I've seen that multiple people have encountered an 'Unknown trimmer' error when using Trimmomatic and unfortunately me too. The code and output I use and receive are written below. CODE: for num in {1121292..1121303...do java -jar /software/shared/apps/x86_64/trimmomatic/0.36/trimmomatic-0.36.jar SE -version 0.36 -phred64 SRR$num.fastq.gz SRR$num.trimmed.fastq.gz ILLUMINACLIP...na…

Trimmomatic RNA-Seq

updated 6.5 years ago • Nottuh

Hi all, I am trying to use Trimmomatic with paired end Illumina transcriptomic data (151 bp reads). I am running the code java -jar /hpc/group/vilgalyslab...jan58/samsa2/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE –phred33 Nash_6890_210407B6/305_S1_L001_R1_001.fastq.gz Nash_6890_210407B6

Illumina Trimmomatic Transcriptomics

updated 3.9 years ago • Jake

Hi! I run trimmomatic java -jar /home/user/program/Trimmomatic-0.39/trimmomatic-0.39.jar SE -phred33 h_2.fastq.gz output2.fastq.gz

dna trimmomatic

updated 4.5 years ago • mailard

Hello everyone, R1: forward R2: reserve DATA: RNA-Seq data i used trimmomatic for paired-end reads. I get 4 outputs. sample.R1.trimmed.fastq, sample.R2.trimmed.fastq, sample.R1.unpaired.fastq

RNA-Seq STAR Trimmomatic

updated 8.1 years ago • xd_d

Dear all, I have a question about the use of trimmomatic. I have used the Illuminaclip step (The one which removes adapters) in trimmomatic even if the QC tool indicated

trimmomatic RNAseq

updated 3.6 years ago • Mozart

Hi, I have trimmomatic 0.39-1 installed via bioconda and I have read the manual. I am confused about giving input files for "paired-end...mode in trimmomatic command lines. I followed up the script and revised it. ` java -jar /opt/anaconda3/pkgs/trimmomatic-0.39-1/share/trimmomatic...SRR}_2_paired.fastq.gz ${SRR}_2_unpaired.fastq.gz ILLUMINACLIP:/opt/anaconda3/pkgs/trimmomatic-0.39-1/share/…

assembly

updated 4.8 years ago • slin023

Hi, I have paired-end read data prepared by illumina Nextera. I'm trying to remove the adapter using Trimmomatic. [illumina adaper sequence manual (p.3)][1] says that the following sequence is used for Read 1 and Read 2 adapter trimming...I have paired-end read data prepared by illumina Nextera. I'm trying to remove the adapter using Trimmomatic. [illumina adaper sequence manual (p.3)][1] says…

sequence next-gen illumina adapter

updated 4.6 years ago • mimi

seen a lot of contradictions Originally my workflow was : FastQC > Confindr > Kraken2 > Trimmomatic (trim adapters + quality) > FastQC > SPAdes. But I have sometimes seen (principally in Biostars) some people using...In my paired end files I have always the same number of reads between R1 and R2. The same after Trimmomatic when i keep the paired files R1 et R2 …

bbnorm trimmomatic

updated 2.8 years ago • valentin.cledassou

I am new in Linux and Trimmomatic , do after installation i need to run it by any specific command **I am using this command:** mohana@monash-Precision...T3600:~$ java -jar ~/Desktop/Farheena/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 8 -phred33 -trimlog FQ-1_log home/desktop/Farheena/41 FQ-1_R1_001.fastq.gz...FQ-1_1P.fq.gz FQ-1_1U.fq.gz FQ-1_2P.fq.gz FQ-1_2U.fq.qz ILLUMINACLIP:/home/…

software error

updated 7.2 years ago • F.I.2011

Hi, I have used Trimmomatic to validate my fastq files, but i have got for outputs , so i wondering which one of them i should use in Tophat or...Hi, I have used Trimmomatic to validate my fastq files, but i have got for outputs , so i wondering which one of them i should use in Tophat or for

RNA-Seq

updated 8.8 years ago • roonymoonlight

35 bp). My final goal is to filter out reads after mapping to a reference genome. I am using Trimmomatic to first trim the adapters. What is a good MINLEN to define for Trimmomatic? The Minimum length I currently defined

Trimmomatic

updated 2.4 years ago • Eliveri

although not all) starts with the triplet "TAA". I assumed these we adapters. However, when I use Trimmomatic with: ILLUMINACLIP:Trimmomatic-0.39/adapters/TruSeq2-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36 These

Trimmomatic

updated 2.9 years ago • ctdarwell

Hi Biostars, I have been using trimmomatic for quite some time, but realized that I don't get something. So one can use LEADING and TRAILING options to remove...the meaning of having TRAILING option if the whole read is scanned? Otherwise, until which base does trimmomatic scan by LEADING option? Cheers

RNA-Seq trimmomatic

updated 5.0 years ago • grant.hovhannisyan

Hi, I am working on small RNA-Seq data analysis, I have query regarding trimmomatic tool which widely used for adapter trimming from reads. In the command below: trimmomatic SE -phred33 input.fastq...Out_trimmomatic.fastq ILLUMINACLIP:/trimmomatic-0.38-1/adapters/TruSeq3-SE.fa:2:30:10 LEADING:30 TRAILING:30 MINLEN:36 TruSeq3-SE.fa its given in software package

RNA-Seq Assembly alignment next-gen sequencing

updated 5.5 years ago • akshay_ware

Hi, Using brew installed trimmomatic/0.38 and run a following script; java -Xms4000M -Xmx12000m -XX:+UseConcMarkSweepGC \ -XX:NewSize=300M -XX:MaxNewSize...300M \ -jar /usr/local/Cellar/trimmomatic/0.38/libexec/trimmomatic-0.38.jar \ PE -threads 24 -trimlog sample1_R1_001.fastq.gz Sample2_R2_001.fastq.gz...Desktop/output_reverse_unpaired.fq.gz\ …

RNA-Seq sequencing

updated 5.9 years ago • akh22

hi i want to use trimmomatic for trimming whole genome sequencing reads (illumina platform), But I've seen that trimmomatic mostly used in...RNA-seq projects. my question: can i use trimmomatic in my whole genome sequencing project

next-gen sequencing

updated 8.3 years ago • reza

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: ![enter image description

rnaseq

updated 3.5 years ago • liuhongran

I have 4 sample of fastaq file each one has two read , i want to use a loop on trimmomatic over them but i face problem with the code: my files are BD143_TGACCA_L006_R1_001.pe.fq.gz BD143_TGACCA_L006_R2_001.pe.fq.gz...t work any help please ? for file in *R1_001.fq.gz; do base=$(basename ${file} _R1_001.fq.gz); trimmomatic PE -threads 1 -phred33 -trimlog trimLogFile -summary stats…

RNA-Seq software error

updated 4.3 years ago • mhwaida258

check the quality of the reads. I found lots of Illumina universal adapters in my reads. Then I used trimmomatic paired-end to trim these overrepresented sequences. After trimming with the trimmomatic, the quality of the...not have those over-represented sequences, but the reverse reads still have them. java -jar trimmomatic-0.39.jar PE -threads 12 PV6N-3_S35_L004_R1_001.fastq.gz PV6N-3_S…

sequence

updated 4.2 years ago • saleh.sereshki

Hi! I received my HiSeq Illumina RNAseq data and want to run trimmomatic to remove bad quality reads and trim adapters. I have used trimmomatic before but I am currently in doubt if I create...for a single sample? A single sample, needs only one adapter with one specific index? Correct? - Trimmomatic needs an adapter file and I will create as follows (with all adapters and indeces in a single f…

Trimming Trimmomatic RNAseq

updated 6.3 years ago • T_18

When I ran the following command, trimmomatic throws me error. cat SRP090879_l.txt | parallel -j 4 "trimmomatic SE -threads 4 [].fastq.gz trimmed/[]_trimmed.fastq.gz

trimmomatic linux

updated 3.0 years ago • nishat04bmb15

Hello, is it possible to assign the final outcome of the trimmomatic command to a variable (or a file)? I am interested in recording the percentage of passed reads, for instance I would...like to get the both surviving percentage -- that is 1.11 -- from the final string given by trimmomatic: ... Input Read Pairs: 11829489 Both Surviving: 131674 (1.11%) Forward Only Surviving: 68519…

sequencing

updated 7.4 years ago • marongiu.luigi

Hi, I have Single 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: java -jar ~/CIRI_v2.0.6...Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 sra_data_SRR1427482.fastq sra_data_SRR1427482 ILLUMINACLIP:TruSeq3

RNA-Seq software error

updated 7.0 years ago • modarzi

Do you think I need to remove them ? I'd like to try to remove this adaptators using Trimmomatic or (fastqX toolkit or cutadapt) I don't want to be too stringent specifying a given length..First I really want to...using Qqual or ReadLength ? Personnaly, I was thinking to use Qual 20 or 115 for readLength/ In [trimmomatic][2] you can remove ILLUMINACLIP:TruSeq3-PE or ILLUMINACLIP:TruSeq2-PE depe…

fastq trimming RNA-Seq Trimmomatic

updated 8.3 years ago • ZheFrench

Hi All, I'm trying to run a script on our university supercomputer, to use Trimmomatic to trim my paired end fastq files before I align them to my ref. genome. I was expecting to get similar outputs to...using is: #!/bin/sh # Grid Engine options (lines prefixed with #$) #$ -N trimmomatic #$ -cwd #$ -l h_vmem=30G #$ -pe sharedmem 2 # Ini…

trimmomatic RNA-Seq

updated 6.4 years ago • matthew.sinton

I have a nextflow script which uses trimmomatic, I am running the script using a conda environment from HPC server. Trimmomatic is able to run however it does now...find the adapter `TruSeq3-PE.fa` that comes with the Trimmomatic package. script: """ trimmomatic \ PE -phred33 \ ${reads[0]} ${reads[1]} \ "trimmed_${pair_id}_R1_paired.fas…

Conda Adapter Nextflow Trimmomatic environment

updated 2.4 years ago • Eliveri

Hello, I have a problem with BGI RNA-Seq files. When doing Trimmomatics, my script stops exactly at sample 41 in each cell's first lane (`V300042149_L01_41_1.fq.gz`) in IlluminaClip...echo $input1 $input2 find . -type f -name V300042149_L01_41_1.fq.gz -prune -o -exec trimmomatic-0.39.jar {} \; java -jar trimmomatic-0.39.jar PE -threads 4 -phred33 \ "$inp…

RNA-Seq next-gen

updated 4.5 years ago • storm1907

Hi everyone, I'm struggling with Trimmomatic on Mac. I'm trying do trim my FastQC file but it giving errors. Maybe my code is not correct I'm not sure. Please help...me. ``` (base) Sehribans-MacBook-Air:~ sehriban$ Trimmomatic PE in_SRR22302419_1.fastq in_SRR22302419_2.fastq out_SRR22302419_1.fastq out_SRR22302419_2.fastq

trim RNA-seq

updated 2.4 years ago • sehriban.buyukkilic

FASTq in PE file but could not figure out the option @ http://www.usadellab.org/cms/index.php?page=trimmomatic Any pointer will be highly appreciated. Thanks

sequence

updated 4.5 years ago • rob.costa1234

I am trying to use Trimmomatic and Bowtie2 on a sample (metagenomic) to do some quality filtering and contaminant screening, the sample has...I am trying to use Trimmomatic and Bowtie2 on a sample (metagenomic) to do some quality filtering and contaminant screening, the sample has been...parallel -j 1 --link 'kneaddata -i {} -o kneaddata_out/ -db /home/shared/bowtiedb/GRCh38_PhiX --trimmomatic /u…

BOWTIE2 Trimmomatic GNU metagenomics parallel

updated 3.4 years ago • johanna

Hi, I'm new to Trimmomatic and need to trim my FASTQ files using Trimmomatic. The tool provides a default adapter file "TruSeq3-PE.fa". Can

next-gen sequencing

updated 6.0 years ago • sruthi

883 results • Page 2 of 18

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