Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cufflinks without reference stopped at chrM

    My code is as simple as this:
    Code:
    cufflinks -o test accepted_hits.bam
    The bam file was generated by tophat. Both tophat and Cufflink are the latest version (1.3 and 1.03).

    Without a reference, cufflinks stop and here is the last output:

    Processing Locus chr9:141152985-141153035 [***************** ]> Processing Locus chrM:0-16571 [************************ ] 97%
    I tried cufflinks (v 1.0.2). I saw the same problem.

    However, if I use cufflinks with a reference, the program runs smoothly without this problem.

    Any suggestion?

    Thanks in advance.
    Last edited by arrchi; 06-09-2011, 10:14 AM.

  • #2
    I checked cufflinks output , there is no chrX, chrY and chrM in the three output files. But my input bam file does have these three chromosome info.

    Any ideas? please!
    Last edited by arrchi; 06-09-2011, 10:15 AM.

    Comment


    • #3
      One of my several cufflinks programs does finished after stuck at chrM for about one day. So i guess it just needs a little bit more time and patience.

      Comment


      • #4
        OK, that's probably because chrM is often overloaded with reads

        Comment


        • #5
          The problem is still there

          And I'm posting this in the year of 2016

          Comment


          • #6
            Originally posted by baritone View Post
            And I'm posting this in the year of 2016
            Even with latest cufflinks version?

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Recent Advances in Sequencing Analysis Tools
              by seqadmin


              The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
              05-06-2024, 07:48 AM
            • 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...
              04-22-2024, 07:01 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 05-14-2024, 07:03 AM
            0 responses
            17 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-10-2024, 06:35 AM
            0 responses
            42 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-09-2024, 02:46 PM
            0 responses
            50 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-07-2024, 06:57 AM
            0 responses
            41 views
            0 likes
            Last Post seqadmin  
            Working...
            X