Question: blast output using -6 format option
0
gravatar for S
5.1 years ago by
S90
United States
S90 wrote:

Hi,

I am running a local blast and save my output using -6 format (tabular). For one hit the result is displayed fine, however for more than one hit, for example when I have two hits, the second result gets appended right at end of the first result (one the same line), I would expect each hit to be on a separate line. How do I get each hit to start on a new line?

Thanks!

blast • 2.1k views
ADD COMMENTlink modified 5.0 years ago by Peter5.8k • written 5.1 years ago by S90
1

Interesting problem! Could you maybe give us details on your OS and the text viewer you're using please? Thank you!

ADD REPLYlink written 5.1 years ago by RamRS25k

Thanks from your question, I figured out that the reason was a text viewer. I was viewing it using notepad, I don't know why in notepad it concatenates the lines. Thanks! 

ADD REPLYlink written 5.1 years ago by S90
1

Notepad in Windows uses CRLF (\r\n) as the line separator. BLAST might be outputting lines split with just LF for same hits and with CRLF or LFLF for new hits.

ADD REPLYlink written 5.1 years ago by RamRS25k
1

I see....Thanks!

ADD REPLYlink written 5.1 years ago by S90
1

Notepad++ and TextPad are good text editors for Windows. 

ADD REPLYlink written 5.1 years ago by onuralp190
1
gravatar for Peter
5.0 years ago by
Peter5.8k
Scotland, UK
Peter5.8k wrote:

Are you running BLAST on Linux/Mac OS but looking at the results on Windows?

If so, the different line ending characters may not be displayed properly. Try using a text editor like NotePad++ under Windows which understands Unix style new lines. See http://en.wikipedia.org/wiki/Newline

ADD COMMENTlink written 5.0 years ago by Peter5.8k
0
gravatar for Bioinformatics_NewComer
5.1 years ago by
Genomic Island
Bioinformatics_NewComer320 wrote:

Did you see A: parsing too large blast result with bioperl OR other methods??

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Bioinformatics_NewComer320
1

I just checked it, I don't think that it answers my question. Thanks for the reply though. Please let me know if my question is not clear. Basically, my second hit result start at the end of the first hit result on the same line right after the first hit result, I would like each result to be on its own line. I am just wondering if this is how blast output the result or there is a parameter setting to solve this.

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by S90
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