CAP3 for DNA assembly
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2.2 years ago
dhananya • 0

I'm using CAP3 for 1st time, I have checked tutorial and gave input file "genome.fasta" as shown below. I have used the below command to run:

cap3 genome.fasta > output.txt 

I got error: Cannot open genome.fasta.

Can anyone pls help to solve this?

>scaffold00017
ATATAAAGCATAAATCGATTAGAAATGAAACCTTCTCAAATCATGAATAagaataatattcttcTAAATGAAGATAAGATTGATCCTAAAGATCTTATGATATTAAAATTAGTAAAAGAATCAGGATAATCTGAATACCGCCGAGGTATTCCATTTAACCCTAAAAAATGTTGAGGAAAAAAAGTCAAATTAACACCTAAAAACATCACTAAAAATTGAGTTTTAAGCACTATTTCATTAAAAGAGATACCAAAAAGTGTTGGAAATCAAAAAGTTACTGCTCCAAAAATAGCAAAAACTGCTCCTATAGATAATACATAATGAAAATGAGCTACTACGTAATAAGTATCATGAAGAATAATATCAATTGAAGAATTAGATAATATAATACCAGTTAATCCCCCCAACGTGAATAAAAataaaaatCCTAAACATCATAATATAGGAGAAT
>scaffold0001
AATATAATTATATATTTACCTGCTCCTTCAAATATCAATTATTTTTGAAACTTAGGGTCTCTTATTGGGATCATATTAATAATTCAAATCGTTTCTGGTTtttttttATCTCTTCATTACTTGTCTTCTATAGAAGAAGCTTTTTATTCAGTTAATCATATCAGCCGAGAAGTATATATAGGGTGATTAGTTCGATTTTTTCATATCAATGGAGCATCGGCTTTTttctttttgattttttctcatattttaaaAAACATTATAAACTCATCATGAAAGTTTACTAATCTGTGAATATCAGGGGTAACCATTCTATTGATTTCTATAGCAACAGCTTTTGTAGGATATGTTTTACCATGAGGCCAAATATCTTTTTGAGCAGCTACTGTAATTACTAATTTAT
>scaffold00011
CCAATATACCAGTAAAAACaaatataatcaa
cap3 • 1.2k views
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Hello dhananya,

Welcome to the forum.

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

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output of ls -lah genome.fa ?

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yes.

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Show actual output. yes is not expected output of the command @Pierre asked for.

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How is that fasta file you show there called? if it's not genome.fasta you will need to give it the name the file has in your case.

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Thank you. Yes I gave name as genome.fasta

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