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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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Adapter sequence input in custom section in config.txt #6

Open arpit20328 opened 5 months ago

arpit20328 commented 5 months ago

So my data is paired end by Illumina in FASTQ.

I used sequence AAAGGGTTT as my forward primer I used sequence CCCAAAGGG as my reverse primer

How do input it in the adapter sequence input line in the config.txt file ?

I used it as following :

adapter? = AAAGGGTTT CCCAAAGGG

is it correct ? if not please let me know...

BioH4z commented 5 months ago

Dear user, you can just put the first part. It will automatically search for the complementary in the paired reads.

arpit20328 commented 5 months ago

@BioH4z my forward and reverse primers sequences are not complementary to each other.

In that case how do I input my adapter sequence in config file ?

BioH4z commented 5 months ago

Dear @arpit20328 , right now, the tool isn't able for search for two adapters that are not complementary. This could be a nice improvement.

A fast solution is to run the trimming part outside HOME-BIO with cutadapt -a and -A options. If you don't want to install cutadapt you can use my docker biohaz/rna-seq and perform the trimming there.

Another quick solution could be to modify the Script.py file (line 1147) and change the line where cutadapt is called with your specific adapters:

os.system("cutadapt -m 20 -a "AAAGGGTTT" -A "CCCAAAGGG" -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).

If you do this, you can also leave the custom adapters in the config file and the script will run the ones that you put in the code.

arpit20328 commented 5 months ago

ok thanks @BioH4z . will try