Hi everyone.
I have a bacterial Illumina Miseq run with forward reads (R1) and another one with reverse reads (R2) in fastq. I have used the fastq.info to obtain the fasta file and the qual file and then I have run trim.seqs which gave me the separated sequences in fasta. However, I cannot make an stability file now, nor make contigs because I have my samples in .fasta and not .fastq... And I do not know how to obtain the .qual of each independent sample. I have being stuck in this step for one week and I cannot find any solution on the internet. Could someone help me please??
Thanks!!
Thanks for you quick response Pritam Kumar Panda
. However, what I got was a single fastq file with all my samples that I converted into one csfasta and qual file including 7 libraries. I could extract the fasta of each individual sample but not the fastq or qual of each individual sample. That is what I need.
You dont have to run fastq.info command, instead you can directly run
make.contigs(ffastq=forward.fastq, rfastq=reverse.fastq, oligos=test.oligos).
Check oligo file format for more details here : https://www.mothur.org/wiki/Oligos_File#Paired_Barcodes
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