CAP3 for DNA assembly
0
0
Entering edit mode
10 weeks 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 • 331 views
ADD COMMENT
0
Entering edit mode

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!

ADD REPLY
0
Entering edit mode

output of ls -lah genome.fa ?

ADD REPLY
0
Entering edit mode

yes.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thank you. Yes I gave name as genome.fasta

ADD REPLY

Login before adding your answer.

Traffic: 1810 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6