Unconfigured Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • gkamath
    Junior Member
    • Apr 2014
    • 4

    Reverse complementary reads in Mummmer

    The repeat-match program in mummer, claims to return reverse complementary repeats, and mark them with 'r'. However, I found that the repeats returned are complementary repeats, not reverse complementary.

    For example if position 10-14 in my sequence are AAGG and position 20-24 are TTCC, these are not reverse complementary repeats but mummer repeats them. Am I doing something wrong here?

    Further, do complementary repeats even matter in genome assembly. Reverse complementary repeats matter, but I do not think complementary repeats should matter as the reads we get from the forward and reverse strands are in opposite directions.

    Edit: sorry the title should have been Reverse complementary repeats in Mummer, rather than Reverse complementary reads in Mummer.
    Last edited by gkamath; 08-05-2014, 11:19 AM. Reason: typo in title

Latest Articles

Collapse

  • GATTACAT
    Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
    by GATTACAT
    Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
    07-01-2026, 11:43 AM
  • SEQadmin2
    Nine Things a Sample Prep Scientist Thinks About Before Sequencing
    by SEQadmin2


    I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

    Here are nine questions we think about, in roughly the order they matter, before...
    06-18-2026, 07:11 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, Yesterday, 11:08 AM
0 responses
7 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 06-30-2026, 05:37 AM
0 responses
11 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 06-26-2026, 11:10 AM
0 responses
19 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 06-17-2026, 06:09 AM
0 responses
53 views
0 reactions
Last Post SEQadmin2  
Working...