Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Lyn Hsiong
    replied
    Originally posted by rhinoceros View Post
    It looks like you're blasting against a protein database and getting hits to CDS (i.e. the gaps represent introns or intergenic regions). If this is the case, you could just extract the ORFs and concatenate them by some simple command like cat. In any case, there must be a one-liner of cat grep cut and awk that would solve your problem..
    thank you for your reply!
    actually, what you mentioned may typify one of the cases. then here i performed a tblastx using two genome sequences and found some of the hits per query had close relationship (certain significant colinearity) although each of the component hits seemed to be less related. so If I arbitrarily set a E/score value I think I will lose some informative hits.
    here I asked a general question for this kind of application, and I hope there is a versatile scripts...

    Leave a comment:


  • rhinoceros
    replied
    It looks like you're blasting against a protein database and getting hits to CDS (i.e. the gaps represent introns or intergenic regions). If this is the case, you could just extract the ORFs and concatenate them by some simple command like cat. In any case, there must be a one-liner of cat grep cut and awk that would solve your problem..

    Leave a comment:


  • how to concatenate blast results (m8) via setting threshold of distance between hits

    hi, dear guys

    I performance blastn (-m 8) using a query file of many sequences, and for each query sequence, the output contains many fragmental hits of significance.

    however, these hits have no overlap, and what is interesting is that most gaps < 300bp (much shorter than full-length of the query sequence).

    so, how can i concatenate those closely related hits into one via setting a value (e.g 300bp) when these hits match the same subject (different regions), ——also to reduce the number of output hits per query.

    for example:



    are there any scripts or tools for this purpose?

    all your replies are welcome!
    Attached Files

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-13-2024, 08:58 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-12-2024, 02:20 PM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-07-2024, 06:58 AM
0 responses
186 views
0 likes
Last Post seqadmin  
Working...
X