outputs of bs_seeker2-build.py

BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data

http://pellegrini.mcdb.ucla.edu/BS_Seeker2/

MIT License

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Closed kwanghoon821 closed 3 years ago

kwanghoon821 commented 3 years ago

Hi, I'm trying to use BSSeeker2.

First, I used bs_seeker2-build.py to build the index.

python bs_seeker2-build.py \ -f path/to/ref.fasta \ --aligner=bowtie2 \ -d outputdir.

I got many outputs(3377) C_C2T.fa C_G2A.fa chr1.data chr1_GL383518v1_alt.data chr1_GL383519v1_alt.data and so on Is this normal?

Anyway, I tried to align using the index.

I have four ".fa" format outputs C_C2T.fa C_G2A.fa W_C2T.fa W_G2A.fa

What should I use file for alignment?

guoweilong commented 3 years ago

Yes, it is normal. Just keep these files, and specify the folder if not build using default parameter.

Best, Weilong Guo

kwanghoon821 commented 3 years ago

@guoweilong Thank you!