Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GenoMax
    replied
    Did you check the headers from the subset BAM files? Those may still contain the offending chromosomes.

    Leave a comment:


  • tirohia
    started a topic removing chromosomes from a bam file.

    removing chromosomes from a bam file.

    I'm trying to upload a bam file, from an alignment to GRCh38 that I've done, to a google genomics dataset, associating it with the reference set for GRCh38. The reason it fails given in the logfile reads:

    Code:
    reference names must be a subset of those of the requested
        reference set: missing ["chr1" "chr10" "chr11" "chr11_KI270721v1_random" "chr12"
        "chr13" "chr14" "chr14_GL000009v2_random" "chr14_GL000194v1_random" "chr14_GL000225v1_random" ...
    It goes on to list another 40 or so fragments. If I do a quick

    Code:
    samtools idxstats cal1.bam
    I do indeed get a whole bunch of chromosome fragments listed. The best I can come up with is that the referenceset on google genomics doesn't like all the fragments, thus the reference names must be a subset message.
    The obvious workaround to test this, is to remove those chromosomes from the bam file. Unfortunately,

    Code:
    samtools view -b cal1.bam chr1 chr2 chr3 > cal-sub-1.bam
    samtools index cal-sub-1.bam cal-sub-1.bai
    samtools idxstats cal-sub-1.bam
    returns a bam file that indeed, removes all the reads from the fragments from the bam file. It still lists the actual fragments though, which in turn, when I try and load to the google genomics dataset, gives me the same error.

    How to I remove all references to the fragments from the bam file? Or is that not what the googlegenomics upload is objecting to.

    Thanks
    Ben.

Latest Articles

Collapse

  • 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
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 05-14-2024, 07:03 AM
0 responses
20 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-10-2024, 06:35 AM
0 responses
44 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
54 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X