How to merge multiple .fasta flies retaining the file headers
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12 months ago
Azuretimes • 0

Hi anyone has an idea about merging multiple .fasta flies retaining the file headers? I tried cat command but it will only keep the 1st header. What I want to do:

FileA

>Header1
Sequence1
>Header2
Sequence2

FileB

>Header3
Sequence3

FileC

>Header4
  Sequence4
>Header5
  Sequence5

What I want:

New File

>Header1
  Sequence1
>Header2
  Sequence2
>Header3
  Sequence3
>Header4
  Sequence4
>Header5
  Sequence5

Thank you so much for your help!

Assembly sequencing • 224 views
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Why do you think cat doesn't work for this?

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Hi Joe, I tried cat, but the problem is that it will only Header1 and lose other header information...

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If you are using it correctly, as per genomax's answer, this cannot happen.

If it is the case, you're doing something else you aren't telling us.

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Hi Joe, thanks for the reply. I followed genomax's answer and it worked finally,

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12 months ago
GenoMax 100k
cat fileA fileB fileC > final_file
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Hi, thanks for the reply. I tried cat, but the problem is that it will only Header1 and lose other header information..

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No it won't. Not unless your files are made on some other OS and don't have correct unix endings. You should try to reformat your files using dos2unix command before cat.

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Thanks for your suggestion! I tried dos2unix and it works!

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You can accept the answer "green checkmark" to provide closure to this thread.

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