Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bam index chromosome size limit

    Hi all,
    I have a question as follows: description of sam/bam/cram file format says that there is a limit to chromosome size in bam file. Above this limit you can't create an index of bam file in bai file format. This limit is 2^29-1, which is circa 500 M.b.p. If at least one chromosome in reference sequence is longer than this limit, indexing fails. I've just tried it out:
    $ samtools index file_sort.bam
    it did fail:
    [E::hts_idx_check_range] Region 536962398..536962445 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6
    [E::sam_index] Read 'NB552414:80:H3WTKBGXK:3:21607:22796:5232' with ref_name='2H', ref_length=665585731, flags=16, pos=536962399 cannot be indexed
    samtools index: failed to create index for "file_sort.bam": Numerical result out of range

    However, never have i encountered any mention of this problem before. It does not occur often - the limit is actually rather high, all human chromosomes, for example, are smaller than this. But for wheat of barley, some chromosomes are actually larger than this limit, thus preventing users from creating indexes in bai format. There is csi format that does not have this size limitation, but it is not as widely used, and vcftools for example does not work with it.
    So, am i just being paranoid, or can this limitation actually prevent user from working on certain genomes as it is? And if it does, how can one overcome it? Split the chromosomes into smaller chunks, of some 300 M.b.p. for example

    Thanks for the help in advance,
    Nick Shmakov, jr researcher, ICG SB RAS

Latest Articles

Collapse

  • 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
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
21 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
46 views
0 likes
Last Post seqadmin  
Working...
X