Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • dpryan
    replied
    52.68% = (2*(4647893+779552+138165) + 510907 + 357302)/(2*11389273)

    Samtools is correct, since if sum the numerator you'll get just under 12 million total alignments, which is exactly what's in the BAM file (14328481-2329052).

    Leave a comment:


  • frymor
    started a topic hisat2 output more reads than are in the file

    hisat2 output more reads than are in the file

    Hi all,
    I am in the middle of testing the hisat2 mapper and encountered a discrepancy between the output hisat2 gives me at the end of the mapping step and the number of reads samtools flagstat counts.

    this is the output I get, when hisat2 is finished:
    Code:
    cat ../hisat2Mapping/WCE7.stat 
    [B]11389273[/B] reads; of these:
      11389273 (100.00%) were paired; of these:
        5961828 (52.35%) aligned concordantly 0 times
        4647893 (40.81%) aligned concordantly exactly 1 time
        779552 (6.84%) aligned concordantly >1 times
        ----
        5961828 pairs aligned concordantly 0 times; of these:
          138165 (2.32%) aligned discordantly 1 time
        ----
        5823663 pairs aligned 0 times concordantly or discordantly; of these:
          11647326 mates make up the pairs; of these:
            10779117 (92.55%) aligned 0 times
            510907 (4.39%) aligned exactly 1 time
            357302 (3.07%) aligned >1 times
    52.68% overall alignment rate
    @Question - how are the 52.68% are calculated? what reads are being considered here as mapped?

    and this is the number of reads I get, when I run samtools flagstat on the sorted/indexed bam file:
    Code:
    samtools flagstat ../hisat2Mapping/WCE7.sorted.bam
    [B]14328481[/B] + 0 in total (QC-passed reads + QC-failed reads)
    2329052 + 0 secondary
    0 + 0 supplementary
    0 + 0 duplicates
    14328481 + 0 mapped (100.00%:-nan%)
    11999429 + 0 paired in sequencing
    6098403 + 0 read1
    5901026 + 0 read2
    10854890 + 0 properly paired (90.46%:-nan%)
    11407498 + 0 with itself and mate mapped
    591931 + 0 singletons (4.93%:-nan%)
    23248 + 0 with mate mapped to a different chr
    18678 + 0 with mate mapped to a different chr (mapQ>=5)
    As you can see, samtools find more reads than there suppose to be originally in the file.

    Is there a simple explanation for that?

    thanks,
    Assa

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, 07:49 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-20-2024, 07:23 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-17-2024, 06:54 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
25 views
0 likes
Last Post seqadmin  
Working...
X