BAM output

[SchulzLab]

Hello, I was wondering whether BatMeth2 can also directly output the alignments in BAM format? Currently I have to sort the alignments with samtools, but the SAM file is really large and creates problems on the hard disks and I have another much bigger dataset, which I am afraid will not be able to be analysed if there is only SAM output.

Thanks for any help, Marcel

[GuoliangLi-HZAU]

Hi Marcel, Thank you very much for your suggestion. We will add this feature to the new version of BatMeth2 as soon as possible. Thanks

[paulstretenowich]

Hi, I'm also very interested about that feature. Is it scheduled to be included in BatMeth2 soon? Thanks, Paul

[ZhouQiangwei]

Hi Paul, The new version of BatMeth2 already can directly output the alignments in BAM format. Thans

[paulstretenowich]

Hi, Sorry, I couldn't find anything about in the doc or in the help menu. Would you explain how to use bam output then? Thanks, Paul

[ZhouQiangwei]

Hi Paul, The default output format of alignment is BAM format. You also can use the '-of [SAM/BAM]' parameter to change the output format. Thanks

[paulstretenowich]

Hi, If I'm using batmeth2-align it's outputting by defaukd a sam file and I can't use -of BAM (not recognized). When using BatMeth2 align it's outputting a sam file:

[ BatMeth2 ] Alignment ... /lb/project/mugqic/analyste_dev/software/BatMeth2/BatMeth2-2.0.1/bin/batmeth2-align -g /lb/project/mugqic/analyste_dev/genomes/species/Homo_sapiens.hg19/genome/batmeth2_index/Homo_sapiens.hg19.fa -p 6 -i data/EMC2-A549-10-days-3D-culture_2-491360_WGBS_E00433_0222_8_S1_L008_R1_001-random0.005.fastq.gz -i data/EMC2-A549-10-days-3D-culture_2-491360_WGBS_E00433_0222_8_S1_L008_R2_001-random0.005.fastq.gz -o EMC2-A549-10-days-3D-culture_2-491360_WGBS-random0.005.sam

Thanks for the help, Paul

[ZhouQiangwei]

Hi Paul, The test shows that the alignment result is output BAM format with samtools by default. Would you please to try if the new version is OK?

BatMeth2 align -g ka -1 s -2 s -o s [ Program directory ] /public/home/ppguan/scheng/software/BatMeth2/bin/ [ Program name ] BatMeth2 [ Workdir ] /public/home/ppguan/qwzhou/arabidopsis_shzky/data/seedling/peakvsTEexp2 [ outputdir ] ./ [ BatMeth2 ] Alignment s, s... /public/home/ppguan/scheng/software/BatMeth2/bin/batmeth2-align -g ka -p 8 -i s -i s | samtools sort -@ 8 -O BAM -o ./s.sort.bam - >> ./s.run.log 2>&1

Thanks

[paulstretenowich]

Hi, I'm using the version 2.0.1 from the release but it seems it's not the right version?

BatMeth2 align -1 data/EMC2-A549-10-days-3D-culture_2-491360_WGBS_E00433_0222_8_S1_L008_R1_001-random0.005.fastq.gz -2 data/EMC2-A549-10-days-3D-culture_2-491360_WGBS_E00433_0222_8_S1_L008_R2_001-random0.005.fastq.gz -g /lb/project/mugqic/analyste_dev/genomes/species/Homo_sapiens.hg19/genome/batmeth2_index/Homo_sapiens.hg19.fa -of BAM -o EMC2-A549-10-days-3D-culture_2-491360_WGBS-random0.005 -p 6 /lb/project/mugqic/projects/pstretenowich_benchmark_genpipes_WGBS/batmeth2 [ Program directory ] /lb/project/mugqic/analyste_dev/software/BatMeth2/BatMeth2-2.0.1/bin/ [ Program name ] BatMeth2 [ Workdir ] /lb/project/mugqic/projects/pstretenowich_benchmark_genpipes_WGBS/batmeth2 [ BatMeth2 ] Alignment ... /lb/project/mugqic/analyste_dev/software/BatMeth2/BatMeth2-2.0.1/bin/batmeth2-align -g /lb/project/mugqic/analyste_dev/genomes/species/Homo_sapiens.hg19/genome/batmeth2_index/Homo_sapiens.hg19.fa -p 6 -i data/EMC2-A549-10-days-3D-culture_2-491360_WGBS_E00433_0222_8_S1_L00 8_R1_001-random0.005.fastq.gz -i data/EMC2-A549-10-days-3D-culture_2-491360_WGBS_E00433_0222_8_S1_L008_R2_001-random0.005.fastq.gz -o EMC2-A549-10-days-3D-culture_2-491360_WGBS-random0.005.sam BatMeth2 v2.00 Read length 75 Max Gap : 200

Thanks, Paul

[GuoliangLi-HZAU]

Hi Paul, Sorry, the release version is not the latest version. I've added a new release version of 'batmeth2-v2.1', or you can download the latest version from git clone. Thanks

[paulstretenowich]

Thanks! Paul