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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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chromosome length #388

Open pxxiao-hz opened 2 years ago

pxxiao-hz commented 2 years ago

Hello， I'm using bowtie2 to align with chromosomes above 2GB and it fails. Is this because of tool limitations? Is there any solution？ Best wishes！

ch4rr0 commented 2 years ago

Hello, a few questions:

What is the format of the read file? How long are the individual reads? What error are you getting? What is your command line?

pxxiao-hz commented 2 years ago

Hi, 1, Hi-C reads. 2, 150 bp. 3&&4, I used Hicpro to deal with hic reads, which uses bowtie2 alignment. Then, I found the bam file doesn't contain the information of two long chromosome, thier length was longer than 2.2GB. One of the commands is: /public/home/software/opt/bio/software/Bowtie2/2.3.4.3/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample1/read_R2_pe.bwt2glob.unmap.fastq --rg-id BMG --rg SM:read_R2 -p 18 -x pe -U rawdata/sample1/read_R2.fq.gz 2>> logs/sample1/read_R2_bowtie2.log| samtools view -F 4 -bS - > bowtie_results/bwt2_global/sample1/read_R2_pe.bwt2glob.bam /public/home/software/opt/bio/software/Bowtie2/2.3.4.3/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample1/read_R1_pe.bwt2glob.unmap.fastq --rg-id BMG --rg SM:read_R1 -p 18 -x pe -U rawdata/sample1/read_R1.fq.gz 2>> logs/sample1/read_R1_bowtie2.log| /public/home/software/opt/bio/software/SAMtools/1.9/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/sample1/read_R1_pe.bwt2glob.bam

Also, I read on bwa's manual that chromosomes can't be more than 2GB in length.