Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Query regarding RNA-Seq hit/read count

    Hi everyone!

    I am running an RNA-Seq experiment and was wondering if anyone could help me with a particular query i had.

    So my RNA-Seq sample had 29,775,906 reads.

    I ran this sample through tophat (no coverage search, unstranded, w/bowtie2). I checked the logs folder in the output and got the following stats :-

    [2013-04-04 10:57:02] Preparing reads
    left reads: min. length=50, max. length=50, 29767088 kept reads (8818 discarded)

    Now, 29767088 + 8818 = 29,775,906 . So until now it makes sense.

    From the bowtie files i got the following information :-

    In,bowtie.left_kept_reads.log

    29767088 (100.00%) were unpaired; of these:
    4316521 (14.50%) aligned 0 times
    17118264 (57.51%) aligned exactly 1 time
    8332303 (27.99%) aligned >1 times

    In,bowtie.left_kept_reads_seg1.log
    4316521 (100.00%) were unpaired; of these:
    3198237 (74.09%) aligned 0 times
    1037571 (24.04%) aligned exactly 1 time
    80713 (1.87%) aligned >1 times

    In bowtie.left_kept_reads_seg2.log
    4316521 (100.00%) were unpaired; of these:
    3177510 (73.61%) aligned 0 times
    1069186 (24.77%) aligned exactly 1 time
    69825 (1.62%) aligned >1 times

    So at this point , correct me if i am wrong, we can conclude :-

    total reads aligned 1 time = 17118264 + 1069186 + 1037571 = 19225021
    total reads aligned >1 time = 8332303 + 80713 + 69825 = 8482841
    But then i converted the accepted_hits.bam file in a .sam file. On this .sam file I did the following two operations :-

    awk '{print $1}' 11129_nc_u.sam | sort | uniq -u | wc -l

    gave me 21638486 (i.e total number of uniques)

    and

    awk '{print $1}' 11129_nc_u.sam | sort | uniq -d | wc -l

    gave me 5519946 (i.e. total duplicates.)

    Now why is the number of uniques from the .sam folder (21638486 ) greater than 19225021 (i.e. obtained from the logs folder)? In the same breath, why is teh number of duplicates from .sam folder (5519946) less than the number in the logs folder (8482841) ?

    Can someone please clarify this point for me?

    Thanks in Advance

Latest Articles

Collapse

  • 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,”...
    Yesterday, 01:16 PM
  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 07:15 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 10:28 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 07:35 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Working...
X