Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Question on reads mapping smallRNA-seq (100% feature coverage)

    Hi all,
    I have a fastq file containing reads from an Illumina NextSeq smallRNA sequencing, a fasta file representing the genome (it is composed by about 33000 sequences with length 18-35 nts), the index and a bed file with coordinates of the genome.
    After adapters trimming the reads are 18-35 nt of length...and I mapped the resulting fastq to the fasta (using either star or bowtie).

    Now I would like to keep ONLY the reads that 100% overlap the features presents in the fasta (I mean that the reads need to be aligned end-to-end to the feature, and the feature has to be covered entirely by the read....so no nucleotides uncovered)...if not, read has to be discarded.

    It seems star aligner and bowtie have no options to do it.....

    I have any idea on how to proceed....could someone help me ?

    Thank you a lot!
    Cristian

Latest Articles

Collapse

  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM
  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-14-2024, 06:13 AM
0 responses
34 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-08-2024, 08:03 AM
0 responses
72 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-07-2024, 08:13 AM
0 responses
81 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-06-2024, 09:51 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X