Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Looking for the sequence of a particular transcript from sequencing data

    First, let me tell you that I'm very new to the field of NGS and not much familiar with the set of tools commonly used for NGS data processing. However, I'm not new to Bioinformatics, and have quite some experience in Linux, Python, Perl , R etc.

    I've to find out the sequence of a particular transcript from a set of mouse fastq files. I've extracted the sequence reads for this particular sequence using bbduk.sh of the bbmap package using the following command:

    Code:
    bbduk.sh  in=/me/clumpedSRA.fq.gz ref=/me/known_transcript.fasta k=13 outm=/me/knownT_reads_only.fastq
    Can somebody tell me how to get the sequence of the transcript from this reads of the sequence of interest? Can any other tools from 'bbmap' be used?

    Besides, I've access to Tophat and Trinity on a high performance cluster.

    Thanks in advance

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X