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FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://felixkrueger.github.io/Bismark/
GNU General Public License v3.0
386 stars 101 forks source link

report on trying bismark_genome_preparation with bowtie2-2.2.6 and hs38DH #6

Closed avilella closed 8 years ago

avilella commented 8 years ago

Downloaded bowtie2 2.2.6 from sourceforge. Downloaded hs36DH from NCBI using bwakit.

grep '^>' hs38DH.fa  | wc -l
3366

Tried bismark_genome_preparation:

$HOME/avilella/Bismark/bismark_genome_preparation --path_to_bowtie $HOME/bowtie2-2.2.6 --bowtie2 $GROUP/Genomes/Human/hs38DH

Successfully ran:

Bismark/bismark_genome_preparation --path_to_bowtie $HOME/bowtie2-2.2.6 --bowtie2 /data/group/test/Genomes/Human/hs38DH                                                  
[user@compute-1-6 hs38DH]$ ls -lrt
total 3725604
-rw-rw-r-- 1 user test 3263690197 Dec  1 10:19 hs38DH.fa
drwxrwsr-x 4 user test         62 Dec  1 11:02 Bisulfite_Genome
[user@compute-1-6 hs38DH]$ tree -Difts
.
[         62 Dec  1 11:02]  ./Bisulfite_Genome
[        227 Dec  1 12:20]  ./Bisulfite_Genome/CT_conversion
[ 1018869605 Dec  1 13:32]  ./Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2
[  760863372 Dec  1 13:32]  ./Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2
[ 1018869605 Dec  1 12:19]  ./Bisulfite_Genome/CT_conversion/BS_CT.1.bt2
[  760863372 Dec  1 12:19]  ./Bisulfite_Genome/CT_conversion/BS_CT.2.bt2
[      40751 Dec  1 11:06]  ./Bisulfite_Genome/CT_conversion/BS_CT.3.bt2
[  760863367 Dec  1 11:06]  ./Bisulfite_Genome/CT_conversion/BS_CT.4.bt2
[ 3263425993 Dec  1 11:05]  ./Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa
[        227 Dec  1 12:17]  ./Bisulfite_Genome/GA_conversion
[ 1018869605 Dec  1 13:26]  ./Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2
[  760863372 Dec  1 13:26]  ./Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2
[ 1018869605 Dec  1 12:16]  ./Bisulfite_Genome/GA_conversion/BS_GA.1.bt2
[  760863372 Dec  1 12:16]  ./Bisulfite_Genome/GA_conversion/BS_GA.2.bt2
[      40751 Dec  1 11:06]  ./Bisulfite_Genome/GA_conversion/BS_GA.3.bt2
[  760863367 Dec  1 11:06]  ./Bisulfite_Genome/GA_conversion/BS_GA.4.bt2
[ 3263425993 Dec  1 11:05]  ./Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa
[ 3263690197 Dec  1 10:19]  ./hs38DH.fa
avilella commented 8 years ago

This was just to report that it worked with recent bowtie2 and recent version of the hs38 reference containing [D]ecoy and [H]aplotype sequences.