Error - adapter trimming

[bioramg]

Hi, I would like to trim adapter sequences from Illumina reads. I read manual and given the output format. But it shows an error when using the following command.

./../../anaconda3/bin/trim_galore --quality -o --/home/Illumina/ . --path_to_cutadapt ./../../anaconda3/bin/cutadapt --paired ./../../forward_1.fastq.gz ./../../reverse_2.fastq.gz

Thank you.

[FelixKrueger]

Hi there, what exactly is the error you are seeing? I would imagine that --quality requires you to specify a quality value (or if you lose this parameter the default quality will be Phred 20).

-o --/home/Illumina/ . This will certainly go wrong as well, as there is no option --/home/illumina/, and the stray . would be interpreted as the first input file, which it isn't.

[bioramg]

Thank you.

Sorry. I am a beginner in bioinformatics. Could you please give correct command to execute?

.trim_galore --quality --/home/Illumina/ . --path_to_cutadapt /bin/cutadapt --paired input_1.fastq input_2.fastq

Is it correct?

[FelixKrueger]

trim_galore --gzip --path_to_cutadapt /bin/cutadapt --paired input_1.fastq input_2.fastq

A command like this might work.

[bioramg]

Thank you. I shall try and inform you. Meanwhile should I use --gzip for fastq.gz files?

[FelixKrueger]

Trim Galore detects whether input files end in .gz, and if so, it will set --gzip automatically. So you may as well not specify it explicitly.

[bioramg]

Thank you.

[aalkin2001]

Hi Felix, I am having an issue with adapter trimming. I ran the following command: trim_galore --illumina --phred33 --fastqc --retain_unpaired --paired K1_R1.fastq K1_R2.fastq K2_R1.fastq K2_R2.fastq W1_R1.fastq W1_R2.fastq W2_R1.fastq W2_R2.fastq -o --output_dir trimmed_fastq

Output response/Result: Please provide an even number of input files for paired-end FastQ trimming! Aborting ... Is there anything I did wrong? Thank you.

[FelixKrueger]

I think the last part of the command is the culprit, as -o --output_dir trimmed_fastq would use --output_dir as the output directory, and then there is a single trailing file called trimmed_fastq.

I think you should be able to shorten the command to:

trim_galore --fastqc  --gzip --output_dir trimmed_fastq *fastq

[aalkin2001]

Thank you, Felix. The command worked.

[FelixKrueger]

Excellent! Good luck!

[bioramg]

Hi, I installed trim-galore and cutadapt through bioconda. My command is: trim_galore --gzip --quality 20 -o /home/trimming/trim . --path_to_cutadapt /home/anaconda3/envs/cutadapt/bin/cutadapt --paired /home/R1.fastq /home/R2.fastq

But I am getting an error like this Multicore support not enabled. Proceeding with single-core trimming. Path to Cutadapt set as: '/home/anaconda3/envs/cutadapt/bin/cutadapt' (user defined) sh: 1: /home/anaconda3/envs/cutadapt/bin/cutadapt: Permission denied Failed to execute Cutadapt porenv perly. Please install Cutadapt first and make sure it is in the PATH, or specify the path to the Cutadapt executable using --path_to_cutadapt /path/to/cutadapt

Then, I included an additional command along with this "-j 2" Path to Cutadapt set as: '/home/anaconda3/envs/cutadapt/bin/cutadapt' (user defined) sh: 1: /home/anaconda3/envs/cutadapt/bin/cutadapt: Permission denied Failed to execute Cutadapt porenv perly. Please install Cutadapt first and make sure it is in the PATH, or specify the path to the Cutadapt executable using --path_to_cutadapt /path/to/cutadapt

Why am I getting this error and how to solve it? Thank you.

[FelixKrueger]

Hmm, can you execute /home/anaconda3/envs/cutadapt/bin/cutadapt on its own? Maybe you need to add another cutadapt at the very end so that you don't point to folder but rather to the executable instead? You will want to see the Cutadapt help text upon entering the command, and if that works, Trim Galore should also work.