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atulkakrana / sPARTA

miRNA-target prediction and PARE-seq based validation tool - uses MapReduce model [Published]
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set -genomeFeature #3

Closed shenweima closed 7 years ago

shenweima commented 7 years ago

Can set -genomeFeature as 0 and 1 at the same time? python3 sPARTA.py -genomeFile IWGSCv1.fa -annoType GTF -annoFile transctipts_merged.gtf -genomeFeature <0/1> -miRNAFile miRNA.fa -libs <SRR1197125.chopped.trimmed.processed.txt SRR1197126.chopped.trimmed.processed.txt > -tarPred -tarScore --tag2FASTA --map2DD --validate -minTagLen 18 -accel 10 An error -bash: 0/1: No such file or directory. How to set?

atulkakrana commented 7 years ago

Hi Shenweima,

No you cannot run sPARTA in both genic and intergenic mode at same time. I would suggest run one (genomeFeature = 0) and rename the folders - 'predicted' and 'output' and then run other ( genomeFeature = 1).

The error is because you have to remove <> from your command. These are used to indicate where an input is required from user. For example, the command to identify genic targets of your miRNAs would be:

python3 sPARTA.py -genomeFile IWGSCv1.fa -annoType GTF -annoFile transctipts_merged.gtf -genomeFeature 0 -miRNAFile miRNA.fa -libs SRR1197125.chopped.trimmed.processed.txt SRR1197126.chopped.trimmed.processed.txt -tarPred -tarScore --tag2FASTA --map2DD --validate -minTagLen 18 -accel 10

Best

Atul

shenweima commented 7 years ago

Thank you . python3 sPARTA.py -genomeFile IWGSCv1.fa -annoType GTF -annoFile transctipts_merged.gtf -genomeFeature 0 -miRNAFile miRNA.fa -libs SRR1197125.chopped.trimmed.processed.txt SRR1197126.chopped.trimmed.processed.txt -tarPred H -tarScore N --tag2FASTA --map2DD --validate -minTagLen 18 -accel 10