For retrieving fastq file from NCBI GEO using GSM number.
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#!/bin/sh | |
if ! type "efetch" > /dev/null; then | |
print "Please install E-utilitie." | |
fi | |
GSM_LIST=$1 | |
GSMs=`cat $GSM_LIST|cut -f1` | |
#echo $SRRs | |
! type "foo" > /dev/null 2>&1; | |
for GSM in $GSMs; do | |
echo $GSM retrieves from NCBI GEO..... | |
SRR=`esearch -db sra -query $GSM |efetch -format docsum |xtract -pattern DocumentSummary -element Run@acc` | |
fastq-dump -A $SRR -O sra_fastq | |
echo fastq-dump done..... | |
done |
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not working
/getFastaFromGEO.sh GSM.List
GSM4432378 retrieves from NCBI GEO.....
unrecognized option: '-f'
fastq-dump done.....