Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Reads length and display in tview

    Hi,

    I had a couple of questions:

    (1) I used the below command to generate the pileup (I created a bowtie index for hg18 & then ran tophat on the sequence data against the UCSC gene annotation "tophat -G hg18.gff3 -i 30 -I 15000 ../bowtie-0.12.5/hg18 s_o_sequence.fastq", the resultant accepted_hits.sam output file was sorted and indexed).
    "samtools*pileup*-vcf*hg18.fa*accepted_hits_sorted.bam*>*accepted_hits_sorted.pileup"

    A couple of lines from accepted_hits_sorted.pileup [The number of reads covering chr1, co-ordinate 747408 (SNP quality score 140) is 28 as per the pileup output]:
    chr1 747408 A M 140 140 60 28 ,,c,ccc,,,,,,c,,,,,,,,,,cccc YWPNKONQQOTWSMHPSGQXXXGGHTJO
    chr1 748086 A M 22 22 60 11 ......^~,^~,^~c^~c^~, WYYXYXESTEI


    Below is a snapshot of what I see when I open tview ("samtools tview accepted_hits_sorted.bam hg18.fa") and navigate to chr1:747408 (the first dotted line appears underlined). I see just 2 reads displayed in the text alignment viewer after I navigate to chr1:747408. Shouldn’t there have been 28 reads?

    747411 747421 747431 747441 747451 747461 747471 747481 747491 747501 747511 747521
    ACCCTGTCTATACTACCTGCCTGTCTAGCAGATCCACCCTGTCTATACTACCTGCCCATCCAGCAGGTCCACCCTGTCTACACTACCTCCCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    ....................................... .............C.........................
    .......................................
    .......................................
    ,,,,,,,,,,,,,c,,,,,,,,,,,,,,,,,,,,,,,,,


    (2) The read length for the sequence data is 33. However, some of the reads displayed in tview are much shorter. Why would that be?
    These are Illumina reads. I used tophat (command used is mentioned above) to generate the accepted_hits.sam from the fastq sequence file. Tophat internally runs the bowtie aligner.
    PS: I have other files wherein I ran BWA, but I haven’t tried viewing them yet using tview.

    Any suggestions/comments will be helpful.

    Thanks in anticipation,
    Veena

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
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X