Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • MAQ's mapview format to binary map format

    maq map aln.map ref.bfa reads.bfq

    maq mapview aln.map > aln.out

    The aln.out is text file and aln.map is binary file.

    I filter some reads in aln.out and want to convert the new aln.out to .map file.

    Because pileup command need .map file.

    How can I convert .out to .map ?

  • #2
    I know of no way outside of a custom script, and I don't know who's written one.

    Alternatively, you could just pool the reads that you want to leave in the set, and redo the map command with only those reads.

    Comment


    • #3
      Originally posted by baohua100 View Post
      maq map aln.map ref.bfa reads.bfq

      maq mapview aln.map > aln.out

      The aln.out is text file and aln.map is binary file.

      I filter some reads in aln.out and want to convert the new aln.out to .map file.

      Because pileup command need .map file.

      How can I convert .out to .map ?
      Why not convert the .map to .sam, then filter, then to .bam. Using the SAM format is probably better supported.

      Comment


      • #4
        Convert .mapview to .map

        Hi everybody!
        I've seen the post is not so current but I hope someone could help me and answer

        I've got the same above problem..that is to have done the alignment by MAQ obtaining the .map file and then converted it in the .mapview file in plain text...

        Now I've filtered some reads acting on the mapview file and i need the .map to call consensus and snp calling by MAQ...

        Coz the conversion to the .sam needed a lot of time (expecially for my files of 35GB each!! ) and i don't trust so much these kind of "masked" conversion..there is nobody who know how to re-obtain the .map binary file of MAQ without redo the alignment (too slowly!!)??

        Thanks a lot!

        Comment

        Latest Articles

        Collapse

        • 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
        • seqadmin
          Current Approaches to Protein Sequencing
          by seqadmin


          Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
          04-04-2024, 04:25 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Today, 08:47 AM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-11-2024, 12:08 PM
        0 responses
        60 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        57 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        53 views
        0 likes
        Last Post seqadmin  
        Working...
        X