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Old 02-10-2015, 06:40 AM   #1
silenus
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Question .fasta and .fa are the same file?

I'm already google but I'm not sure.
Since in BWA tool use .fa as a reference ,and in GATK tool use .fasta .
I already download hs37d5.fa file ,so can I use it to generate .dict and .fai file
to use in gatk or not?

I'm new guy in this field, please help me ,and sorry for my bad english

Thank you,
Silenus
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Old 02-10-2015, 06:45 AM   #2
sarvidsson
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Files ending with ".fa" and ".fasta" (and others, I've also come across ".fas" or ".fna") are typically FASTA files. You should be able to use that file with both BWA and the GATK.
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Old 02-10-2015, 06:58 AM   #3
mbblack
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If in any doubt, just open the file in any ASCII text editor and look at it. The FASTA file format is about as simple a text format as you can get, and easily checked:

http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
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Old 02-10-2015, 07:12 AM   #4
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Quote:
Originally Posted by mbblack View Post
If in any doubt, just open the file in any ASCII text editor and look at it. The FASTA file format is about as simple a text format as you can get, and easily checked:

http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
Opening 3+ GB text files (like human genome FASTA file the TO mentioned) with a standard text editor will most certainly use up all the RAM and typically render the computer inresponsive - not a very good idea! If you working in a command line environment, use "less" or something similar to look at the file.
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Old 02-10-2015, 08:03 AM   #5
silenus
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Quote:
Originally Posted by sarvidsson View Post
Files ending with ".fa" and ".fasta" (and others, I've also come across ".fas" or ".fna") are typically FASTA files. You should be able to use that file with both BWA and the GATK.
Oh I got it ,thank you sir @sarvidsson
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Old 02-10-2015, 08:05 AM   #6
silenus
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Quote:
Originally Posted by mbblack View Post
If in any doubt, just open the file in any ASCII text editor and look at it. The FASTA file format is about as simple a text format as you can get, and easily checked:

http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
haha , by the way thanks for your comment @mbblack
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Old 02-10-2015, 09:13 AM   #7
mbblack
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Quote:
Originally Posted by sarvidsson View Post
Opening 3+ GB text files (like human genome FASTA file the TO mentioned) with a standard text editor will most certainly use up all the RAM and typically render the computer inresponsive - not a very good idea! If you working in a command line environment, use "less" or something similar to look at the file.
Yes, I wasn't specifically thinking of the size of the specific file in question, but my point was that if you simply look at the first few lines of any text file you'd know whether it was in FASTA format or not. The extension is a meaningless reference, as I have had people send me files named "foo.fa" that were not at all actual FASTA files.
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