Hello, and sorry if this question is in the wrong section of the forum or if the answer is obvious to all but me...
I am new to using bowtie2 (2.2.0), aligning ~ 300,000 single-end 454 cDNA reads to a de-novo transcriptome. I am finding that changing the value for -k results in a dramatic change in the overall alignment rate, but it is my understanding that the -k option should only change the number of alignments reported, and not the percentage of reads which have at least one valid alignment.
With all other options as default, and only changing the value for -k, I find the following:
without -k specified (default)
22.69% of reads aligned exactly 1 time
60.52% of reads aligned > 1 times
83.20% overall alignment rate
-k 2
22.23% of reads aligned exactly 1 time
61.70% of reads aligned > 1 times
83.92% overall alignment rate
-k 10
22.02% of reads aligned exactly 1 time
62.25% of reads aligned > 1 times
84.26% overall alignment rate
-k 200
22.02% of reads aligned exactly 1 time
62.29% of reads aligned > 1 times
84.31% overall alignment rate
Granted, this is a small change overall (a few tenths of a percent), but this becomes a bit more dramatic when I use the some settings recommended for RSEM (--very-sensitive --dpad 0 --gbar 99999999 --mp 1,1 --mp 1 --score-min L,0,-0.1) except that -k is varied
-k 2
15.92% of reads aligned exactly 1 time
24.93% of reads aligned > 1 times
40.86% overall alignment rate
-k 10
15.78% of reads aligned exactly 1 time
28.06% of reads aligned > 1 times
43.84% overall alignment rate
-k 200
15.89% of reads aligned exactly 1 time
30.25% of reads aligned > 1 times
46.14% overall alignment rate
-k 1000
15.89% of reads aligned exactly 1 time
30.27% of reads aligned > 1 times
46.16% overall alignment rate
Why do these values change? From reading the manual I believe that the only change will be in the maximum number of alignments per read that get reported. To my mind, a read still has an alignment regardless of whether you report only 1 alignment for that read, or up to 1000, so that the overall alignment rate should not change.
Hoping that someone can shed some light on this. Thanks
I am new to using bowtie2 (2.2.0), aligning ~ 300,000 single-end 454 cDNA reads to a de-novo transcriptome. I am finding that changing the value for -k results in a dramatic change in the overall alignment rate, but it is my understanding that the -k option should only change the number of alignments reported, and not the percentage of reads which have at least one valid alignment.
With all other options as default, and only changing the value for -k, I find the following:
without -k specified (default)
22.69% of reads aligned exactly 1 time
60.52% of reads aligned > 1 times
83.20% overall alignment rate
-k 2
22.23% of reads aligned exactly 1 time
61.70% of reads aligned > 1 times
83.92% overall alignment rate
-k 10
22.02% of reads aligned exactly 1 time
62.25% of reads aligned > 1 times
84.26% overall alignment rate
-k 200
22.02% of reads aligned exactly 1 time
62.29% of reads aligned > 1 times
84.31% overall alignment rate
Granted, this is a small change overall (a few tenths of a percent), but this becomes a bit more dramatic when I use the some settings recommended for RSEM (--very-sensitive --dpad 0 --gbar 99999999 --mp 1,1 --mp 1 --score-min L,0,-0.1) except that -k is varied
-k 2
15.92% of reads aligned exactly 1 time
24.93% of reads aligned > 1 times
40.86% overall alignment rate
-k 10
15.78% of reads aligned exactly 1 time
28.06% of reads aligned > 1 times
43.84% overall alignment rate
-k 200
15.89% of reads aligned exactly 1 time
30.25% of reads aligned > 1 times
46.14% overall alignment rate
-k 1000
15.89% of reads aligned exactly 1 time
30.27% of reads aligned > 1 times
46.16% overall alignment rate
Why do these values change? From reading the manual I believe that the only change will be in the maximum number of alignments per read that get reported. To my mind, a read still has an alignment regardless of whether you report only 1 alignment for that read, or up to 1000, so that the overall alignment rate should not change.
Hoping that someone can shed some light on this. Thanks
Comment