Prepare data description file
BAMLINK need the data description textfile, which defines all the necessary information. A typical project might involve the assembly of more than one library with different insert sizes. The description file tells how to interpret the input files. An simple example with a single library looks like this:
bam1 /netscratch/dep_tsiantis/arm_intermediate/ath1k_intermediate/PA6928/PA6928.round.1.bam * 216 0.157870 0 15 0.700000
- library id always use "bam*" if bam file is used.
- sequence type PAIRENDED for paired-end reads (FR -> <-); MATEPAIR for mate-pair reads (RF <- ->)
- bamfile the bam file containing all aligned reads which will be used for scaffolding.
- groupid defines group id of the reads in the bam file which will be used for this round of scaffolding. Use "*" if all reads will be used.
- insert size defines the average insert size
- insert size standard error
- minimum links defines the minimum links for a reliable scaffold
- ratio of links defines the minimum minimum ratio of links for a reliable scaffold
- the insert size of short fragments in a mate-pair library The reads mapped to a position whose distance to either end of a reference contig is shorter than this value will be excluded from scaffolding (optional, for mate-pair library only)