Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Count number of genes matched for each primer pair - Bowtie2 - samtools

    HI,
    I'm running the following bowtie2 command to identify proper pairs matching my database. I have added the no-mixed since i only want proper pairs (no single mates). No mismatches for the moment as specified by -N0

    ALL_forward.fna: A fasta list of forward primers
    ALL_reverse.fna : A fasta list of reverse primers

    Code:
    bowtie2  -N0 -a  --no-mixed --fr  --minins 450 --maxins 1500 -x database -1 ALL_forward.fna -2 ALL_reverse.fna  > out.sam
    Here is the output. In this case i can see that primer f_109 and r_209 have full matches to different genes of my database. How can i count how many genes are targetted by each primer pair.

    Ideally the ouput should be:
    Primer-pair Nb_hits Seqs
    f_109-r_209 5 ATAAGCTCACGA-CGGAACTGCACG

    which means that primer pair f_109-r_209 has targets 5 genes in my database and the output sequences.

    Since i have different primers how can i get this information from the output ??

    Code:
    f_109   99      JQ337711.1.1426 112     0       12M     =       578     478     ATAAGCTCACGA    IIIIIIIIIIII    AS:i:-6 XS:i:-6 XN:i:0  XM:i:1
            XO:i:0  XG:i:0  NM:i:1  MD:Z:6C5        YS:i:-6 YT:Z:CP
    r_209   147     JQ337711.1.1426 578     0       12M     =       112     -478    CGGAACTGCACG    IIIIIIIIIIII    AS:i:-6 XS:i:-6 XN:i:0  XM:i:1
            XO:i:0  XG:i:0  NM:i:1  MD:Z:11T0       YS:i:-6 YT:Z:CP
    f_109   355     JX227029.1.1518 168     0       12M     =       645     489     ATAAGCTCACGA    IIIIIIIIIIII    AS:i:-6 XS:i:-6 XN:i:0  XM:i:1
            XO:i:0  XG:i:0  NM:i:1  MD:Z:6C5        YS:i:-6 YT:Z:CP
    r_209   403     JX227029.1.1518 645     0       12M     =       168     -489    CGGAACTGCACG    IIIIIIIIIIII    AS:i:-6 XS:i:-6 XN:i:0  XM:i:1
            XO:i:0  XG:i:0  NM:i:1  MD:Z:2A9        YS:i:-6 YT:Z:CP
    thanks for any help,
    Last edited by danova; 07-20-2015, 07:50 AM.

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