Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Convert Sam file with incorrect fields to Fastq using HTSeq

    Hello,

    I am working with BAM/SAM files generated by MapSplice on (human) RNA-seq paired-end reads from Illumina HiSeq. I want to convert them into fastq in order to realign them (I don't have access to the raw data).

    To do this I am trying to use HTSeq-0.5.4p3 with python2.7 using
    for a in HTSeq.bundle_multiple_alignments(samfile):
    a[0].read.write_to_fastq_file(myfqfile)

    The problem is that these Sam files have incorrect Sam fields and I get the error
    ValueError: ("Malformed SAM line: MRNM == '*' although flag bit &0x0008 cleared").
    The same error is raised with the picard tool SamToFastq.

    I know this is a normal error since the Sam files are incorrect but I wanted to know if someone had a workaround for this problem?
    I will eventually work on a script to reformat correctly all the Sam files but if someone has one I would be very happy to have it!

    Thanks,
    Anne
    Last edited by AnneBiton; 06-05-2013, 02:44 PM.

  • #2
    You could try 'samtools fixmate' or similar to deal with errors like this in the MRNM field, but it sounds like there could be a bug in MapSlice if it produces invalid SAM/BAM files.

    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, 06-14-2024, 07:24 AM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-13-2024, 08:58 AM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-12-2024, 02:20 PM
    0 responses
    17 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-07-2024, 06:58 AM
    0 responses
    185 views
    0 likes
    Last Post seqadmin  
    Working...
    X