Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How to map SOLiD paired end reads by Bfast

    1. I found that bfast localalign can't support -1 and -2 options. So I'm confused how it works in
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

    My bfast version is 0.6.4e. Is -1 and -2 work in other versions?

    2. Then I tried to merge 2 paired end fastq files into 1 file and run bfast match. But in the bfast postprocess step how to set -r ReadGroup.txt? Could you please show an simple example?

    3. The MAPQ of sam files generated by bfast is also Phred scaled, right? If so I can set an cutoff to filter them.
    Thanks a lot for you help and time!

  • #2
    Originally posted by beliefbio View Post
    1. I found that bfast localalign can't support -1 and -2 options. So I'm confused how it works in
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

    My bfast version is 0.6.4e. Is -1 and -2 work in other versions?
    Check out the bfast+bwa version to get that functionality (I assumed you used the bwa functionality instead of bfast match).

    For clarity, if you wish to use BWA's "bwa aln" functionality for paired end reads, then you need to align each end independently, merging them together in "bfast localalign" with the "-1/-2" options. Otherwise, the paired end reads should be merged (automatically in solid2fastq) into one fastq file to be processed by "bfast match".

    Originally posted by beliefbio View Post
    2. Then I tried to merge 2 paired end fastq files into 1 file and run bfast match. But in the bfast postprocess step how to set -r ReadGroup.txt? Could you please show an simple example?
    See the SAM spec on how to create an RG line.

    Originally posted by beliefbio View Post
    3. The MAPQ of sam files generated by bfast is also Phred scaled, right? If so I can set an cutoff to filter them.
    Thanks a lot for you help and time!
    You can set a cutoff to filter them yes. Better (higher) mapq should correlate with higher stringency.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      New Genomics Tools and Methods Shared at AGBT 2025
      by seqadmin


      This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

      The Headliner
      The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
      03-03-2025, 01:39 PM
    • seqadmin
      Investigating the Gut Microbiome Through Diet and Spatial Biology
      by seqadmin




      The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...
      02-24-2025, 06:31 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Today, 12:50 PM
    0 responses
    9 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-03-2025, 01:15 PM
    0 responses
    181 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-28-2025, 12:58 PM
    0 responses
    275 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-24-2025, 02:48 PM
    0 responses
    663 views
    0 likes
    Last Post seqadmin  
    Working...
    X