Trying to use fasta as an input

[Former user]

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!

[Mohammad Rostami]

use command -F at the end

[Kornel Labun]

use -f

[Stephane Plaisance]

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