Hello,
I have aligned my RNA-Seq paired-end data to a reference using Bowtie2:
Bowtie2 -x Ref -1 pair1.fq -2 pair2.fq -S out.sam
In order to calculate RPKM we need to know the total number of mappable reads in the experiment which was obvious in the case of single end data. I am confused now which number to use as "mappable reads in the experiment" in the case of paired-end data. This is Bowtie2 alignment summary
19231140 reads; of these:
19231140 (100.00%) were paired; of these:
1790875 (9.31%) aligned concordantly 0 times
4367667 (22.71%) aligned concordantly exactly 1 time
13072598 (67.98%) aligned concordantly >1 times
----
1790875 pairs aligned concordantly 0 times; of these:
30148 (1.68%) aligned discordantly 1 time
----
1760727 pairs aligned 0 times concordantly or discordantly; of these:
3521454 mates make up the pairs; of these:
2645377 (75.12%) aligned 0 times
322397 (9.16%) aligned exactly 1 time
553680 (15.72%) aligned >1 times
93.12% overall alignment rate
Thank you in advance!
I have aligned my RNA-Seq paired-end data to a reference using Bowtie2:
Bowtie2 -x Ref -1 pair1.fq -2 pair2.fq -S out.sam
In order to calculate RPKM we need to know the total number of mappable reads in the experiment which was obvious in the case of single end data. I am confused now which number to use as "mappable reads in the experiment" in the case of paired-end data. This is Bowtie2 alignment summary
19231140 reads; of these:
19231140 (100.00%) were paired; of these:
1790875 (9.31%) aligned concordantly 0 times
4367667 (22.71%) aligned concordantly exactly 1 time
13072598 (67.98%) aligned concordantly >1 times
----
1790875 pairs aligned concordantly 0 times; of these:
30148 (1.68%) aligned discordantly 1 time
----
1760727 pairs aligned 0 times concordantly or discordantly; of these:
3521454 mates make up the pairs; of these:
2645377 (75.12%) aligned 0 times
322397 (9.16%) aligned exactly 1 time
553680 (15.72%) aligned >1 times
93.12% overall alignment rate
Thank you in advance!
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