Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowie12Beta mapping direction restriction or bug?

    Dear all, I was trying to map 76nt reads using Bowtie. I wanted to use the "seed" feature to avoid trimming off the adapter sequence.

    1) this is the sequence that I trimmed off the last "4nt" long "adapter", which is not really the adapter, and I got it mapped.
    HWUSI-EAS1621.1.2.1.5.745.0 16 chr1 173833971 255 72M * 0 0 CATCAGATAGGAGCGAAAGACTTAATATTGCTCATCAGCGTTAGTCTGCTGAACTATGTTATCATCATTGTA ;:;143>>=9:>:+=A?B78A?BBAB@@@=B<AA@B@;?0>BA8>A@7@ABB<BBBABBAA?:?BACCBABB XA:i:0 MD:Z:72 NM:i:0

    2) so now I map the non-trimmed 76nt sequence, it turned out unmapped.
    HWUSI-EAS1621.1.2.1.5.745.0 4 * 0 0 * * 0 0 TACAATGATGATAACATAGTTCAGCAGACTAACGCTGATGAGCAATATTAAGTCTTTCGCTCCTATCTGATGATCT BBABCCAB?:?AABBABBB<BBA@7@A>8AB>0?;@B@AA<B=@@@BABB?A87B?A=+:>:9=>>341;:;<919 XM:i:0

    my parameters: -q -n 3 -l 30 -k 10 --solexa1.3-quals --best -S -y
    So here is the thing: the seed length is 30nt, and is a perfect match(on reverse strand), so it ought to be reported. But why not?

    Thanks in advance!

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin


    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
    Today, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
37 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
41 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
35 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
54 views
0 likes
Last Post seqadmin  
Working...
X