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chhylp123 / BitMapperBS

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
Apache License 2.0
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output problem #2

Open freshlearner opened 5 years ago

freshlearner commented 5 years ago

Hi i tested BitMapperBS recently ,it was really an ultrafast and memory-efficient aligner. i runned the software successfully.but i have same problems with the output. the output didn't contain Methylation information .but just report the alignment info ,how can i get the the Methylation information ?

here is my command: /opt/software/BitMapperBS-master/bitmapperBS --search /data/project/Program_zhouj/BS-seq_test/BitMapperBS/genome_index/Tibetan.fa --seq1 /data/project/Program_zhouj/BS-seq_test/BitMapperBS/test/SA_0226_S_24_1.clean.fq --seq2 /data/project/Program_zhouj/BS-seq_test/BitMapperBS/test/SA_0226_S_24_2.clean.fq --pe -t 4 -o SA_0226_S_24

chhylp123 commented 5 years ago

Hi i tested BitMapperBS recently ,it was really an ultrafast and memory-efficient aligner. i runned the software successfully.but i have same problems with the output. the output didn't contain Methylation information .but just report the alignment info ,how can i get the the Methylation information ?

here is my command: /opt/software/BitMapperBS-master/bitmapperBS --search /data/project/Program_zhouj/BS-seq_test/BitMapperBS/genome_index/Tibetan.fa --seq1 /data/project/Program_zhouj/BS-seq_test/BitMapperBS/test/SA_0226_S_24_1.clean.fq --seq2 /data/project/Program_zhouj/BS-seq_test/BitMapperBS/test/SA_0226_S_24_2.clean.fq --pe -t 4 -o SA_0226_S_24

Now you can use MethylDackel (https://github.com/dpryan79/methyldackel) to extract methylation information. For example, if you have the the ouput file of BitMapperBS named output.sam:

(1) Converting SAM directly to a sorted BAM file; samtools sort -@ 4 -o output.bam output.sam (SAMtools version 1.3 or newer, using 4 CPU threads) or samtools view -bS output.sam | samtools sort - -o output.bam (SAMtools version 1.2 or older)

(2)Extract methylation information using 4 CPU threads: MethylDackel extract reference_genome.fa output.bam -@ 4

I am now also developing a new methylation extract algorithm. For the next several days, the new version of BitMapperBS will be resleased to directly output the methylation information rather than .sam or .bam.

Thank you for the interest in BitMapperBS.

freshlearner commented 5 years ago

Hi i tested BitMapperBS recently ,it was really an ultrafast and memory-efficient aligner. i runned the software successfully.but i have same problems with the output. the output didn't contain Methylation information .but just report the alignment info ,how can i get the the Methylation information ? here is my command: /opt/software/BitMapperBS-master/bitmapperBS --search /data/project/Program_zhouj/BS-seq_test/BitMapperBS/genome_index/Tibetan.fa --seq1 /data/project/Program_zhouj/BS-seq_test/BitMapperBS/test/SA_0226_S_24_1.clean.fq --seq2 /data/project/Program_zhouj/BS-seq_test/BitMapperBS/test/SA_0226_S_24_2.clean.fq --pe -t 4 -o SA_0226_S_24

Now you can use MethylDackel (https://github.com/dpryan79/methyldackel) to extract methylation information. For example, if you have the the ouput file of BitMapperBS named output.sam:

(1) Converting SAM directly to a sorted BAM file; samtools sort -@ 4 -o output.bam output.sam (SAMtools version 1.3 or newer, using 4 CPU threads) or samtools view -bS output.sam | samtools sort - -o output.bam (SAMtools version 1.2 or older)

(2)Extract methylation information using 4 CPU threads: MethylDackel extract reference_genome.fa output.bam -@ 4

I am now also developing a new methylation extract algorithm. For the next several days, the new version of BitMapperBS will be resleased to directly output the methylation information rather than .sam or .bam.

Thank you for the interest in BitMapperBS.

Thank you very much ,i'll try this software right away!