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BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
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Build Index Name Changed #22

Open pzhang312 opened 5 years ago

pzhang312 commented 5 years ago

Hello,

I ran the code python /dir/bs_seeker2-build.py -f MyGenome -d /out/dir/ --aligner=bowtie2 -p /u/local/apps/bowtie2/2.2.9 In MyGenome there is a contig named Seg3751.2; however, the index has Seg3751_2 instead of Seg3751.2. Did I do anything wrong that resulted in this name change? When I tried to use MethylDackle mbias on my bam files I got an error saying 'Seg3751_2 could not be found in the reference genome'. So I'd like to keep the names consistent. What is the best course of action for me? Can I just rename Seg3751_2.data to Seg3751.2.data and do the mapping again?

Thank you!

guoweilong commented 5 years ago

Hi @pzhang312 ,

It is a bug, has been fixed since version v2.1.7

So I suggest you try to install the newest releases link.

Best, Weilong

======== V2.1.7 - Oct. 23, 2018

  1. [bsutils/utils.py] : fix a bug in chromosome name such as converting '.' to ''