Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • aloliveira
    replied
    Hello,

    The Blast ignore that sequences, there is a lower-complexity filter by default on BLAST to avoid miss-called bases or masked bases (normally N or X correspondingly). You can turn-off that parameter if you want.

    Best regards,
    André.

    Leave a comment:


  • rdu
    replied
    Hi apratap,

    Thank you. Your anwser sounds reasonable. If I know some related futher, will also share with you. Have a nice day.

    Leave a comment:


  • apratap
    replied
    Hi rdu

    I see these messy N's always in the Illumina data. I think it could mean variety of different things but this is just my interpretation. Mianly I think when the base caller is not able to decipher which nucleotide to call it leaves "N" behind. If you see bunch of N a the end it could relate to falling quality. However if you see a long stretch in the middle, it could also mean complexity in that genomic region.

    HTH
    -Abhi

    Leave a comment:


  • rdu
    started a topic "N"s in DNA sequence data

    "N"s in DNA sequence data

    I found there're many "N"s in a initial DNA genome sequence data, like:

    CTGAAATCACTACTTTCCTTGTTAGGCTCGGCGCATGTGTTAAGTAGNNN
    NTTATANNCNGNNNAGNATTTATNNNNNNNNCTTNNNNNNCGGTTATATG

    What's the explanation for it? I took BLASTX allignment, no error messages popped up, then how BLAST treats them? Thanks.

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 10:28 AM
0 responses
7 views
0 likes
Last Post seqadmin  
Started by seqadmin, Today, 07:35 AM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 02:06 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-14-2024, 07:03 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Working...
X