blast output using -6 format option

Question

[S]

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!

[Ram]

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

[S]

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!

[Ram]

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.

[S]

I see....Thanks!

[onuralp]

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

[Bioinformatics_NewComer]

Did you see this?

[S]

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.

Answer 1

[Peter]

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