About Mapping Efficiency of Bisulfite aligners

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4.9 years ago

chaudharyc61 ▴ 100

Hello everyone, I am working with my own Bisulfite data generated as single-end reads. So, when i'm using Bs-seeker2 i'm getting a mapping efficiency of approx 75-80% but at the same time if i'm using Bismark or BSMap aligner the mapping efficiency get down by 30%. I can't understand the why it is happening,. Any help??

Organism : Arabidopsis thaliana

Read Lenght : 75

bismark command: bismark --genome_folder path-to-genome --se  file1.fq  -non_directional --bowtie2 --parallel 4 -N 1 -L 20 -o Mapped/default

Thank you in advance Chandan

alignment Bisulfite-sequencing • 1.4k views

ADD COMMENT • link updated 2.8 years ago by francesca3 ▴ 150 • written 4.9 years ago by chaudharyc61 ▴ 100

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Details missing: Read length, organism, command lines. Please see [ Please read before posting a question ] -- How To Ask A Good Question

ADD REPLY • link 4.9 years ago by ATpoint 85k

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Were you able to resolve this? I am also observing low mapping efficiency with BSMap. Any help would be great. Thanks in advance.

ADD REPLY • link 3.7 years ago by Pinki • 0

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HI, did you solve this problem? I have the same problem too. Thank you

ADD REPLY • link 2.8 years ago by francesca3 ▴ 150

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