Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • parser for sam?

    hello all

    I'm newbie and need advices..

    this is my first post here in seqanswers. help me out.

    what i'm trying to do is find DEGs in differently stress-treated groups.

    what i have been done are like this...

    i have raw seqs from 454 and sanger of each stress group.

    i've done pre-processing job so they are ready to be assembled.

    i combined clean reads of each group into one fasta file then i ran iAssembler.

    iAssembler gave me sam file and consensus file as an ouput.

    what i want to do is

    extract origin of reads distribution from unigene..

    like unigene one consists # of reads from stress group 1, # of reads from stress group2.. and so forth..

    not sure that i made myself clear. forgive my poor english

    want to know is this possible what i'm trying to do?

    and is there any parser that can achieve what i'm trying to do?

    thank you guys in advance.

  • #2
    Hi.
    Why do you combine stress-treated groups? You can run iAssembler in each groups.
    If there is a special reason to combine the reads, you can add tags to the read names using sed Linux command. After that you can easily identify your reads in the final SAM file.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Exploring the Dynamics of the Tumor Microenvironment
      by seqadmin




      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
      07-08-2024, 03:19 PM
    • seqadmin
      Exploring Human Diversity Through Large-Scale Omics
      by seqadmin


      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
      06-25-2024, 06:43 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Today, 07:20 AM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-16-2024, 05:49 AM
    0 responses
    33 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-15-2024, 06:53 AM
    0 responses
    37 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-10-2024, 07:30 AM
    0 responses
    41 views
    0 likes
    Last Post seqadmin  
    Working...
    X