Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • TopHat extremely low paired mapping rate. PLS HELP!

    Hey guys, I have some problems with my paried-end RNA seq analysis on Galaxy. As you can see in the bam flagstat output, my tophat alignment rate is very low.

    15620641 + 0 in total (QC-passed reads + QC-failed reads)
    0 + 0 duplicates
    15620641 + 0 mapped (100.00%:-nan%)
    15620641 + 0 paired in sequencing
    7109757 + 0 read1
    8510884 + 0 read2
    503768 + 0 properly paired (3.23%:-nan%)
    2938970 + 0 with itself and mate mapped
    12681671 + 0 singletons (81.19%:-nan%)
    0 + 0 with mate mapped to a different chr
    0 + 0 with mate mapped to a different chr (mapQ>=5)

    So this is Hiseq 100X100 PE run on mouse samples. I QC'ed by fastq using quality trimmer (>=30) and masker (>=20) and they look fairly good. I estimated the inner distance of mate paris to be 250+-200, based on a Bowtie alignment. All other parameters were kept as default.

    Can anyone tell me why they pair so badly? Could it be adaptor contamination?

Latest Articles

Collapse

  • 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
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
66 views
0 likes
Last Post seqadmin  
Working...
X