Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • the tophat generate the bam file instead of sam files?

    I have a question:

    when i trying to use tophat (to alignment in order to generate the SAM file when can be loaded into the cufflinks.Why the output only gives me bam files in the default sub-directories? Is there any way to generate the SAM file? or i have used the wrong parameters? I am using tophat 1.1.0

    Thanks!

  • #2
    bam to sam conversion is easy with samtools

    Code:
    samtools view -h myfile.bam > myfile.sam
    In any case, the current version of cufflinks will accept BAM, but the online documentation doesn't seem to reflect that yet. But I just successfully ran a bunch with bam as input (successfully=cufflinks ran; I haven't looked at the output yet).

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Latest Developments in Precision Medicine
      by seqadmin



      Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

      Somatic Genomics
      “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
      Today, 01:16 PM
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Today, 07:15 AM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 10:28 AM
    0 responses
    15 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 07:35 AM
    0 responses
    16 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-22-2024, 02:06 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Working...
    X