Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cmccabe
    started a topic 40x reads calculation

    40x reads calculation

    Attached is the original output from bedtools (zipped file) and a custom file using the awk code below in which the average reads per bait are calculated (average.txt)

    Code:
     awk '{if(len==0){last=$4;total=$6;len=1;getline}if($4!=last){printf("%s\t%f\n", last, total/len);last=$4;total=$6;len=1}else{total+=$6;len+=1}}END{printf("%s\t%f\n", last, total/len)}' output.bam.hist.txt > average.txt
    Is it possible to output the length of the bait, average # of reads, and the # calculated for 40x coverage? I am not sure how to do this.

    The awk will do the first 2 things (length of bait and average # of reads), but I am not sure how to accomplish the last part (calculate the 40x coverage). Thank you .
    Attached Files
    Last edited by cmccabe; 06-11-2015, 10:48 AM.

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:46 AM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-24-2024, 11:09 AM
0 responses
24 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
159 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
127 views
0 likes
Last Post seqadmin  
Working...
X