Help with cd-hit

Question

[jaspreetk.dhanjal]

Can any one please tell me if we can view alignment between the query and the hits obtained when using cd-hit-est-2d. It is difficult to guess the position of mismatches and gaps using the current format.

Thanks in advance!!

Answer 1

[5heikki]

You mean

   -p   1 or 0, default 0
    if set to 1, print alignment overlap in .clstr file

?

[jaspreetk.dhanjal]

No, not really this option. What I need is a detailed alignment between the query and the hits obtained showing the position of matches, mismatches and gaps.

[5heikki]

Not very well documented (i.e. at all), but to see the alignments, apparently you have to compile cd-hit yourself with MAKEALIGN macro defined. How to define it? I have no clue..

[jaspreetk.dhanjal]

I found this post but it does not work. Nothing more is available in the same context.

[5heikki]

Post your issue to https://github.com/weizhongli/cdhit/issues

[jaspreetk.dhanjal]

Thanks a lot for the suggestion!