Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • I would like to know basic pipeline for analysis of miRNA from SOLID seq data ?

    We have raw data in COLOR space format (.csfasta) and would like to profile and analyze it in order to find known and novel miRNA in sample. Further we are also looking for Diff. expression between two samples.
    Any suggestion ???
    Actually i am facing problem to handle directly from .csfasta because as per my survey, i know many tools (web serivces/offline tool ) but No one or very few able to handle .csfasta file for analysis of mapping,known,novel and diff exp.

    Thanks & looking forward for your valuable input.

  • #2
    abi had their own tool called RNA2MAP.

    Comment


    • #3
      Use Life Tech's LifeScope 2.5 and that will get you the mapping and the count data that you need for subsequent differential expression analysis

      Comment


      • #4
        Originally posted by unique379
        to do so...i got fastq output in decode format cs2bs (without 5' primer T and 3' adapter)...

        Now i am trying to align this fastq output with Bowtie with this command line arguments..(what i got from here: http://seqanswers.com/forums/showthread.php?t=3775)

        bowtie --sam -q -a -n 0 -l 15 -e 99999 -k 200 --chunkmbs 1024 --best...

        But i am not sure that i am in right way.....??

        could someone suggest me to align this fastq with right option of bowtie in order to get best alignment ?? or is that correct arguments ??
        Hi Unique379,

        I am confused with your comment regarding getting fastq format in decode format? There are some serious conversion issues if one directly converts color space to base space. Much better if you leave everything in color space, and this means you will have to index the reference in colorspace (using the -C parameter in bowtie-build).

        Did you know you can use bowtie to map with existing csfasta + qual data files? Here is an example of a command line we have previously used:

        bowtie -C -f --integer-quals -l 21 -n 1 --nomaqround --chunkmbs 256 --best --col-cqual --col-keepends --sam --quals input.qual bowtie_ref_index input.csfasta output.sam

        You (and others) might be interested in a new software tool I have developed to help analyse miRNA data. Visit miRspring.victorchang.edu.au for detailed information. The website describes the miRspring document as well as providing some basic information on preparing BAM files.

        Good luck! Would be interested to hear your findings when comparing to lifescope output.

        D

        Comment

        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
        32 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
        80 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