table of contents
| FASTAQ-TO_TILING_BAM(1) | User Commands | FASTAQ-TO_TILING_BAM(1) |
NAME¶
fastaq_to_tiling_bam - Make a BAM file of reads uniformly spread across the input reference
DESCRIPTION¶
usage: fastaq_to_tiling_bam [options] <infile> <read_length> <read_step> <read_prefix> <outfile>
Takes a sequence file. Makes a BAM file containing perfect (unpaired) reads tiling the whole genome
positional arguments:¶
- infile
- Name of input fasta/q file
- read_length
- Length of reads
- read_step
- Distance between start of each read
- read_prefix
- Prefix of read names
- outfile
- Name of output BAM file
optional arguments:¶
- -h, --help
- show this help message and exit
- --qual_char QUAL_CHAR
- Character to use for quality score [I]
- --read_group READ_GROUP
- Add the given read group ID to all reads [42]
Important: assumes that samtools is in your path
| February 2017 | fastaq 3.15.0 |