Trying to use fasta as an input
Issue #2
resolved
Hi, I'm trying to use a fasta file instead of a target gene or genomic region but it insists on needing the Target argument: chopchop.py: error: argument -Target/--targets is required What should I do? Thanks!
Comments (3)
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- changed status to resolved
use -f
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HI Kornel,
I am also exploring the option to use fasta as query but having the file eGFP.fa in the current folder
eGFP_vect.fa
>eGFP_vect ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGAC GGCGACGTAAACGGCCACAAGTTCAGCGTGTCTGGCGAGGGCGAGGGCGATGCCACCTAC GGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACC CTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAG CAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTC TTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTG GTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCAC AAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAAC GGCATCAAGGCGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCC GACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCAC TACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTC CTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAA
these commands fails:
chopchop.py -rm1perfOff -G hg38 -F eGFP_vect.fa chopchop.py -rm1perfOff --genome hg38 --fasta eGFP_vect.fa usage: chopchop.py [-h] -Target TARGETS [-r] [-D DATABASE] [-e EXON_NUMBER] [-TDP TARGETDOWNSTREAMPROMOTER] [-TUP TARGETUPSTREAMPROMOTER] [-G GENOME] [-g GUIDE_SIZE] [-c] [-SC] [-BB BACKBONE] [-R5 REPLACE_5P] [-t TARGETREGION] [-T {1,2,3,4}] [-taleMin TALEMIN] [-taleMax TALEMAX] [-nickaseMin NICKASEMIN] [-nickaseMax NICKASEMAX] [-offtargetMaxDist OFFTARGETMAXDIST] [-f FIVEPRIMEEND] [-n ENZYME_CO] [-R MINRESSITELEN] [-v MAX_MISMATCHES] [-m MAX_HITS] [-M PAM] [-o OUTPUT_DIR] [-F] [-p PADSIZE] [-P] [-3 PRIMER3OPTIONS] [-A PRIMERFLANKS] [-DF DISPLAYSEQFLANKS] [-a GUIDEPADDING] [-O LIMITPRINTRESULTS] [-w] [-J] [-nonO] [-scoringMethod {XU_2015,DOENCH_2014,DOENCH_2016,MORENO_MATEOS_2015,CHARI_2015,G_20,KIM_2018,ALKAN_2018,ZHANG_2019,ALL}] [-repairPredictions {mESC,U2OS,HEK293,HCT116,K562}] [-rm1perfOff] [-isoforms] [-filterGCmin FILTERGCMIN] [-filterGCmax FILTERGCMAX] [-filterSelfCompMax FILTERSELFCOMPMAX] [-consensusUnion] [-BED] [-GenBank] [-offtargetsTable] chopchop.py: error: argument -Target/--targets is required
What am I missing here?
Could you please add a more command examples in the README to cover this kind of case.
Thanks
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use command -F at the end