Can mapreads deal with paired end reads?

[zhanxw]

mapreads documentation does not mention how to map paired end reads.
Does anyone have any experience?

[lmf_bill]

not, for paired-end reads, you can firstly do single-end reads mapping by "mapreads", then "pairing" can be used for pairing.

[zhanxw]

do you know where to find "pairing" documentation?
I found some options are not hard to understand, e.g. "flen", "rlen", "Z" (from pairing options below).
I hope SOLiD gives more examples in the future....

pairing(V2.5:06/09/2009) R3file F3file lower upper [M=mode][f=flen][r=rlen][Z=(L1,U1);(L2,U2)...][S=refseq] [O=0/1] [U=0/1] [T=##] [X=matrix] [F=maskingF] [R=maskingR] [G=0/1][I=##][D=##][i=##][d=##][P=0/1][q=##][V=tmp_res_file][z=maxrescue][a=TreshR][b=TreshF][B=##][E=##][u=snprate][H=iubmapping][A=VA][m=mis_p][L=min_len][h=histogramFile][x=dropscore][y=indelcutoff][o=outfile][np=#processors]
M=mode (default 0): 0 R3-F3 pairing; 1: F5-F3 pairing
O=0 sorted order; O=1 pairing by order(1st w 1st, 2nd w/ 2nd & so on)
U=0 all non-rescued pairs (default), U=1 only unique non-rescued pair
UR=0 all rescued pairs (default), UR=1 only unique rescued pair (default)
Uh=0 for histograms, include all pairs, Uh=1 only include unique pairs in histogramT=## is the cutoff for rescue output
P=0/1 i/o format 0 pos.mis, 1: chrom_pos.mis
q= number of rescued alignments
B,E specify the beginning and ending penal numbers;
A=0/1 whether treat Valid adjacent as 1
H=0/1 whether allow IUB mapping

[JDS]

http://solidsoftwaretools.com, you can download the corona_lite software package ( mapreads included ) and the documentation.
you can find the pairing part, as well as the SNP and small indel.

[zhanxw]

I found the documentation! Thanks, JDS.