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carlferr / HOME-BIO

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities)
GNU Lesser General Public License v3.0
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Adapters not trimmed #7

Open arpit20328 opened 3 months ago

arpit20328 commented 3 months ago

I have paired end fastq file which has 2 adapters

Forward primer: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA Reverse primer: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

Please tell me which lines of Script.py needs to be changed for trimming

Following lines are with cutadapt . I DID following modifications. :

line 1147: os.system("cutadapt -m 20 -a "+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA+" -A "+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT+" -j "+n_thread+" -o "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_a[0]+"_trimmed.fastq -p "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_b[0]+"_trimmed.fastq "+inputfile_a+" "+inputfile_b)

line 2124: os.system("cutadapt -m 20 -a "+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA+" -j "+n_thread+" -o "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_a[0]+"_trimmed.fastq "+inputfile_a)

line 3094: os.system("cutadapt -m 20 -a "+adapter+" -A "+adapter+" -j "+n_thread+" -o "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_a[0]+"_trimmed.fastq -p "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_b[0]+"_trimmed.fastq "+inputfile_a+" "+inputfile_b)

AM I DOING IT RIGHT ?

BioH4z commented 3 months ago

Dear @arpit20328 , if your sequences are paired-end it isn't necessary to modify line 2124 but you should modify line 3094 if your sequences are DNA. My suggestion is to modify lines 1147 and 3094. If you have any problems, please, let us known continuing the discussion in the same "issue".

arpit20328 commented 3 months ago

Hi @BioH4z

I am getting following error: when modified only 3094 and 1147

3094: os.system("cutadapt -m 20 -a "+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA+" -A "+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT+" -j "+n_thread+" -o "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_a[0]+"_trimmed.fastq -p "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_b[0]+"_trimmed.fastq "+inputfile_a+" "+inputfile_b)

1147: os.system("cutadapt -m 20 -a "+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA+" -A "+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT+" -j "+n_thread+" -o "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_a[0]+"_trimmed.fastq -p "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_b[0]+"_trimmed.fastq "+inputfile_a+" "+inputfile_b)

line 2124: os.system("cutadapt -m 20 -a "+adapter+" -j "+n_thread+" -o "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_a[0]+"_trimmed.fastq "+inputfile_a)

image

BioH4z commented 3 months ago

Dear @arpit20328 , you should remove the quotes and the +:

line 1147 os.system("cutadapt -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -j "+n_thread+" -o "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_a[0]+"_trimmed.fastq -p "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_b[0]+"_trimmed.fastq "+inputfile_a+" "+inputfile_b)

line 3094 os.system("cutadapt -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -j "+n_thread+" -o "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_a[0]+"_trimmed.fastq -p "+split_output_path+"/2_Fastq_trimmed/"+sample_only_name_b[0]+"_trimmed.fastq "+inputfile_a+" "+inputfile_b)

arpit20328 commented 3 months ago

@BioH4z

Great it worked