diff --git a/bin/getFastqFromSraPaired b/bin/getFastqFromSraPaired index ad8cb5b..b09a1e1 100755 --- a/bin/getFastqFromSraPaired +++ b/bin/getFastqFromSraPaired @@ -17,7 +17,7 @@ if [ ! -f "./${runId}.sra" ] ; then exit 1 fi -fastq-dump -B -I --split-files ./${runId}.sra +fastq-dump -B --defline-seq '@$si/$ri' --defline-qual '+' --split-files ./${runId}.sra if [ ! -f "${runId}_1.fastq" -o ! -f "${runId}_2.fastq" ] ; then echo "fastq-dump didn't work as expected? ${runId}_{1,2}.fastq expected" diff --git a/bin/getFastqFromSraSingle b/bin/getFastqFromSraSingle index 5f7b510..f87f944 100755 --- a/bin/getFastqFromSraSingle +++ b/bin/getFastqFromSraSingle @@ -16,7 +16,7 @@ if [ ! -f "./${runId}.sra" ] ; then exit 1 fi -fastq-dump -B -I --split-spot --skip-technical ./${runId}.sra +fastq-dump -B --defline-seq '@$si' --defline-qual '+' --split-spot --skip-technical ./${runId}.sra if [ ! -f "${runId}.fastq" ] ; then echo "fastq-dump didn't work as expected? ${runId}.fastq expected"