Combined Forward and Reverse fastaq files from EBI_ENA

Question

[galud1990]

Hello all,

I have a bunch of data that I have downloaded from EBI-ENA, however I only get a big fastaq file for each sample and I think Forward and Reverse are Combined together. I would like to get a forward and reverse reading fasta q file. I've read that when geeting data from ena or ncbi the fastaq R1 and R2 are together in one file. if anyone has suggestions into how to get fastaq R1 and R2 I would appreciated it. I am going crazy trying to figure out how to get these sequences.

This is the code I used to get my data:

#!/bin/bash

# download_ebi_fastq.sh
#

 for study_accession in ERP021896 ERP020023  ERP006348
 do
count=-1

curl -s "https://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=${study_accession}&result=read_run&fields=secondary_sample_accession,submitted_ftp" | grep -v "^secondary_sample_accession" > ${study_accession}.details.txt

for fq in `awk '{print $1, $2}' ${study_accession}.details.txt`
do
    ((count++))
    if [[ $(( count % 2)) -eq 0 ]]
    then
        id=$fq
        current_path=${study_accession}/${id}
        current_base=${current_path}/${id}

        if [ -d "${current_path}" ]; then
            continue
        fi
        echo "Fetching ${id}..."

        mkdir -p ${current_path}
        curl -s "http://www.ebi.ac.uk/ena/data/view/${id}&display=xml" > ${current_base}.xml &
    else
        if [ -e "${current_base}.fna" ]; then
            continue
        fi

        # sed from http://stackoverflow.com/a/10359425/19741
        curl -s $fq | zcat > ${current_base}.fq &
    fi

    if [[ $((count % 10)) -eq 0 ]]
    then
        wait
    fi
done

done

wait

[WouterDeCoster]

Off topic, but the format is a "fastq" file. Not fastaq, that does not exist. The majority of people will understand what you mean, but correct terminology facilitates communication.

[galud1990]

yes, got it. Sorry about that!

[GenoMax]

It appears that those are single end runs. So you are going to get only one read. SRA example and ENA examples.

[galud1990]

Yes I realized that after I post this. I toolay missed that. Thanks for your response!