Hi All,
I am here to look for acceptable solutions for my goals of short reads mapping.
Goal 1: mapping short reads as fast as possible
Goal 2: if number of mapped reads is low, improve it
Goal 3: try to eliminate false positive mapping
For goal 1, I've evaluated some tools like Bowtie, BWA, BFAST, SSAHA2,etc. Bowtie wins for the speed and robust. BWA and BFAST report errors.
But the mapped result did not satisfy me with around 20% mapped to transcriptome.
To improve the number of mapped reads. The methods I though are:
Method 1: make QC and cut off 3 end basepairs (I cut off 25 of 100 according to QC result). It can improve ~4%, totally ~24%
Method 2: adjust Bowtie parameters, from v=2 to v=3. It can only improve ~1% ;use y option, but cost 2 times of v=2
Method 3: use a more sensitive tool to remap unmapped reads.Say, use bfast or smalt or maq.
One considering is how to handle false positive mapping?
I wonder what's your solutions for this kind of issue?
Thanks.
I am here to look for acceptable solutions for my goals of short reads mapping.
Goal 1: mapping short reads as fast as possible
Goal 2: if number of mapped reads is low, improve it
Goal 3: try to eliminate false positive mapping
For goal 1, I've evaluated some tools like Bowtie, BWA, BFAST, SSAHA2,etc. Bowtie wins for the speed and robust. BWA and BFAST report errors.
But the mapped result did not satisfy me with around 20% mapped to transcriptome.
To improve the number of mapped reads. The methods I though are:
Method 1: make QC and cut off 3 end basepairs (I cut off 25 of 100 according to QC result). It can improve ~4%, totally ~24%
Method 2: adjust Bowtie parameters, from v=2 to v=3. It can only improve ~1% ;use y option, but cost 2 times of v=2
Method 3: use a more sensitive tool to remap unmapped reads.Say, use bfast or smalt or maq.
One considering is how to handle false positive mapping?
I wonder what's your solutions for this kind of issue?
Thanks.
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