The dtype of the loom file layers - if more than 6000 molecules/reads per gene per cell are expected set uint32 to avoid truncation (default run_10x: uint16) -d, -dump ¶įor debugging purposes only: it will dump a molecular mapping report to hdf5. The logic to use for the filtering (default: Default) -M, -multimap ¶ gtf file containing intervals to mask -l, -logic ¶ Table containing metadata of the various samples (csv fortmated rows are samples and cols are entries) -m, -mask ¶ (4 processors per node with 8 cores each, and I guess 4 threads spawning on each core.) My sysadmin speculates that this is inefficient with regard to memory. The dtype of the loom file layers - if more than 6000 molecules/reads per gene per cell are expected set uint32 to avoid truncation (default run_dropest: uint32) -d, -dump ¶ gtf file containing intervals to mask (Optional), -samtools-threads ¶ The sample name that will be used as a the filename of the output. The logic to use for the filtering (default: Default) -o, -outputfolder ¶ Otherwise an error will be thrown -l, -logic ¶ If –bcfile is not specified the file will be searched in the default position outputted by velocyto tools dropest_bc_correct. Set the vebosity level: -v (only warnings) -vv (warnings and info) -vvv (warnings, info and debug) If p is prepended a more complete (but huge) pickle report is printed (default: 0) -v, -verbose ¶ The dtype of the loom file layers - if more than 6000 molecules/reads per gene per cell are expected set uint32 to avoid truncation (default run: uint32) -d, -dump ¶įor debugging purposes only: it will dump a molecular mapping report to hdf5. no-PG Do not add a PG line to the header of the output file. By default, operation is single-threaded. The number of MB used for every thread by samtools to sort the bam file -t, -dtype ¶ INT Set number of sorting and compression threads. If fewer threads are desired, they can be specified with the -jobs flag, e.g. Bgzip-compressed and tabix-indexed file with annotations. Where mybams.fofn is a file of BAM files, and genome.fa.fai is the output of samtools faidx or alternately a newline separated list of chromosomes. Add or remove annotations.-a, -annotations file. My server has more than 1 CPU, so why isnt using more. The option is currently used only for the compression of the output stream, only when -output-type is b or z. I am running samtools view by specifying multiple threads, however, the CPU never goes above 100. The number of threads to use to sort the bam by cellID file using samtools -samtools-memory ¶ Use multithreading with INT worker threads. Since the rule bwamap needs 8 threads, only one job of the rule can run at a time, and the Snakemake scheduler will try to saturate the remaining cores with other jobs like, e.g., samtoolssort. (Default: no) -M, -multimap ¶Ĭonsider not unique mappings (not reccomended), -samtools-threads ¶ If set to bp the first N bases of the sequence will be used to extend UB (ideal for STRT). If set to Gene then the GX tag will be appended to the UB tag. If set to chr the mapping position (binned to 10Gb intervals) will be appended to UB (ideal for InDrops+dropEst). In case UMI is too short to guarantee uniqueness (without information from the ampping) set this parameter to chr, Gene ro bp If this flag is used the data is assumed UMI-less and reads are counted instead of molecules (default: off) -u, -umi-extension ¶ The logic to use for the filtering (default: Default) -U, -without-umi ¶ Important: cells reads should not be distributed over multiple bamfiles is not supported!! (default: off) -l, -logic ¶ If this flag is used every bamfile passed is interpreted as an independent cell, otherwise multiple files are interpreted as batch of different cells to be analyzed together. In order to reduce disk access, the output of Bowtie was piped into SAMtools, thus converting SAM output to BAM format on the fly. gtf file containing intervals to mask -c, -onefilepercell ¶ Table containing metadata of the various samples (csv formatted, rows are samples and cols are entries) -m, -mask ¶ The sample name that will be used to retrieve informations from metadatatable -s, -metadatatable ¶
Thread support first arrived in version 0.1.19 (March 2013), which enabled them for sorting and BAM file writing in the view command. Output folder, if it does not exist it will be created. SAMtools has also become faster, most notably by gaining the ability to use threads to take better advantage of the parallelism available on modern multicore systems. If –bcfile is not specified all the cell barcodes will be included.Ĭell barcodes should be specified in the bcfile as the CB tag for each read -o, -outputfolder ¶