Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie output files

    Hi!

    I am trying to replicate some biocomputational procedures from a scientific paper related to ChIP-Seq data. When using bowtie as the alligner and introducing the output (specified as .sam format) in the MACS software it tells me that the file format is not recognized.
    However, after converting the unrecognized sam file to bam format using samtools, MACS does recognize the file format and starts analyzing the data.

    Could anyone shed some light on this?

    My bowtie and macs commands are:

    bowtie -m 2 -q -p 24 --sam hg19 File1.fastq File1.sam

    macs14 callpeak -t File1.sam -c ControlFile.sam
    -n ExperimentName -S -g hs --pvalue 1e-9 --keep-dup=auto



    Iñigo

  • #2
    Using the --format command in MACS will insist on the input files being in a given format. It is possible that by using the default automatic format detection that MACS got confused by your file.

    That is my best guess and solution.

    Comment


    • #3
      You should switch to MACS2 anyway.
      MACS2 might recognize the format correctly.
      Otherwise, I would specify the format explicitly as westerman suggested, and also check the header and the first entries of the SAM file for any potential problems with the file.

      You're also using 24 threads during the alignment with Bowtie. If you don't have that many processors available, the output can be mixed up. Of course, if you do have the 24 processors available on your machine, then you should be using the 24 threads to do the alignment quickly.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Best Practices for Single-Cell Sequencing Analysis
        by seqadmin



        While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
        06-06-2024, 07:15 AM
      • 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,”...
        05-24-2024, 01:16 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 07:24 AM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-13-2024, 08:58 AM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-12-2024, 02:20 PM
      0 responses
      16 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-07-2024, 06:58 AM
      0 responses
      184 views
      0 likes
      Last Post seqadmin  
      Working...
      X