I have a bunch of PAF files that I would like to use with samtools mpileup to recover the read coverage for a given a list of genomic position. *Those PAFs are the results of ONT reads alignments against a reference. As mpileup works with SAM/BAM format I would like to convert my PAF...
SAMtools可以将.sam文件转换为.bam文件(其是SAM文件采用GZIP算法压缩的二进制文件),因此加载和读取都很快。转换SAM文件为BAM文件之后,需要进行排序(sorted),以便当程序想查找在某个位点的reads时,不必搜索整个BAM文件。 先看看samtools帮助手册: http://www./doc/samtools.html (1).sam转为.bam: samtools view -b...
Dear QuasR team, I am facing a problem during SAM to BAM convertion. I am using QuasR to align bisulfite converted DNA on the Drosophila dm6 genome. alignment files missing - need to: create 2 genomic alignment(s) Testing the compute nod...
将sam 转换为 bam(并再次返回)Created: November-22, 2018 Samtools 可用于在 sam 和 bam 之间进行转换:-b 表示输入文件将采用 BAM 格式 -S 表示标准输出应该是 SAM 格式 samtools view -sB thing.bam > thing.sam 并在山姆和巴姆之间转换:samtools view thing.sam > thing.bam samtools sort thing.ba...
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sam文件转换为bam 代码语言:javascript 复制 samtools view-Soutput.sam-Obam-o output.bam bam文件排序 代码语言:javascript 复制 samtools sort output.bam-@16-Obam-o output.sorted.bam 计算覆盖度 代码语言:javascript 复制 bioconvert bam2cov output.sorted.bam output.cov ...
Other options successful with coordinate sorted input (but not all functions require it). Two error types, depending on the "convert to" datatype BED Yaml
samtools_file_convert.pl - script to convert alignment files between SAM and BAM file formats.=head1 SYNOPSISsamtools_file_convert.pl --i input_file --f input_file_format --opt options (1|2|3|4|) [--r reference_fasta_file] [--o output_dir] [--sb samtools_bin_dir] [--sv ...