Question: Tophat: Proper-Paired Reads
gravatar for ai
7.3 years ago by
ai0 wrote:

Hi Everyone,

I tried Tophat v 2.0.6 and GSNAP v 2013-02-05 to align Illumina paired-end reads. However, the numbers of proper-paired reads were very different. I also used cufflinks for assembly, but got similar number of genes/isoforms. Is there anything wrong with my commands? Why did Tophat result in such low rates of proper-paired reads? Thanks!

To get proper-paired reads: samtools view -f 0x2 accepted_hits.bam | cut -f1 | sort | uniq | wc -l

Tophat comands:

tophat -G genes.gtf -o tophat --no-novel-juncs genome read_1 read_2

Results: 1,431,500 (6.34%) proper-paired reads; 3746 genes (cufflinks).

GSNAP command

gsnap -A sam -N 0 -D ~/Software/gmap-2013-02-05/ -d mm10 -s mm10.splicesites.iit read_1 read_2

Results: 20,543,759 (90.9%) proper-paired reads;3959 genes (cufflinks).

tophat • 2.1k views
ADD COMMENTlink modified 7.3 years ago by Ashutosh Pandey12k • written 7.3 years ago by ai0
gravatar for swbarnes2
7.3 years ago by
United States
swbarnes28.2k wrote:

Isn't cut f1 | uniq going to compress two properly paired reads into a single read name?

What does samtools flagstat accepted_hits.bam tell you is the # of properly paired reads?

ADD COMMENTlink written 7.3 years ago by swbarnes28.2k
gravatar for Ashutosh Pandey
7.3 years ago by
Ashutosh Pandey12k wrote:

Well this is not an answer but you should try '-c' to count. For e.g. samtools view -c -f 0x2 accepted_hits.bam. It should give you the counts of the properly paired mapped reads.

ADD COMMENTlink written 7.3 years ago by Ashutosh Pandey12k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 996 users visited in the last hour