Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • zebrafisch
    replied
    Originally posted by jtladner View Post
    I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?

    Jason


    splitBam is part of the bamUtil package, which i found it here https://github.com/Homebrew/homebrew-science and it was very easy to download it.

    Leave a comment:


  • kmcarr
    replied
    Originally posted by danielsbrewer View Post
    SplitBam looks ideal, but I can't find a download link for it. Any ideas?

    And thanks for the other suggestion too, that makes a lot of sense.

    --EDIT--
    Actually it looks like there are no @RG in the headers ... Oh Dear.
    Originally posted by jtladner View Post
    I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?

    Jason
    Go here and either follow the instructions for retrieving the current development release from the source repository or download the tarball for the latest stable realese (0.1.4). Note that either way you are downloading the entire libStatGen toolkit, which you must then compile. SplitBam is merely one of the programs in the toolkit.

    Leave a comment:


  • jtladner
    replied
    SplitBam download link?

    I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?

    Jason

    Leave a comment:


  • danielsbrewer
    replied
    SplitBam looks ideal, but I can't find a download link for it. Any ideas?

    And thanks for the other suggestion too, that makes a lot of sense.

    --EDIT--
    Actually it looks like there are no @RG in the headers ... Oh Dear.
    Last edited by danielsbrewer; 09-29-2011, 01:03 AM.

    Leave a comment:


  • Chipper
    replied
    If the lane info is stored in RG tags you can use this: http://genome.sph.umich.edu/wiki/SplitBam

    Leave a comment:


  • gringer
    replied
    When I did this a few days ago (with only knowledge of command-line stuff and samtools), here's a rough guide to what I did:
    1. Extract header from BAM file
      Code:
      samtools view -H infile.bam > header.sam
    2. filter out lanes from BAM file, add header
      Code:
      (cat header.sam; samtools view infile.bam | grep '^DATA...._<lane>_.') > out_lane<lane>.sam
    3. convert SAM to BAM
      Code:
      samtools view -S out_lane<lane>.sam -b > out_lane<lane>.bam


    There's probably some better way, but it would have taken longer for me to find than for me to just do it and deal with the additional overhead of storing temporary SAM files per lane.

    Leave a comment:


  • Convert merged BAM back to per lane BAM or FASTQ file

    I have got some illumina data in a a merged BAM file for a particular sample and I would like to convert it back to per lane data files (BAM or fastq) so it would be compatible with the analysis pipeline. Any ideas on the best way to do this?

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