Hi Peter, I've attached a shell script for making the TAB files from the miraconvert produced sam file which has been depadded (instructions for depadding are given in the script). The script tries to make 5 libraries and tells you which ones have paired reads in them. Also, I just found a problem in the sam file produced in the version 4.0 of miraconvert when making the sam file from the maf. So you need to use miraconvert from version 4.0rc4 (release candidate #4) to make the sam file which makes the sam file correctly. I'll post a new thread about this. Regards Robert
Attachment:
SAM-SSPACE-OUT.sh
Description: Binary data
On 14 Feb 2014, at 3:07 am, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote: > Hi Robert, Andreas, etc. > > On 22 Oct 2013, at 23:15 , Robert Willows <robert.willows@xxxxxxxxx> wrote: >> I've been trying to get paired end position and contig information from >> paired end and mate paired libraries in a MIRA assembly to create a >> SSPACE tab file for scaffolding. >> >> ... > > It wasn't obvious how to give the tab file to SSPACE from the command > line - I read the Perl code then noticed it was in the manual - the tab file > goes in the library file like this: > > Lib1 file1.1.fasta file1.2.fasta 400 0.25 FR > Lib1 file2.1.fasta file2.2.fasta 400 0.25 FR > Lib2 file3.1.fastq file3.2.fastq 4000 0.5 RF > Lib2 TAB file4.tab 4000 0.5 RF > Lib3 TAB file5.tab 10000 0.5 RF > >> I realize I can just reuse SSPACE with the original libraries which will map >> the reads with bowtie. I don't want to do this as MIRA has done a much >> better job at placing the reads so I just want to use the position >> information >> in a tab file for scaffolding. > > Also SSPACE v2.0 ignores any reads with N in them before calling bowtie, > and so unlike MIRA it seems to need pre-trimmed FASTQ read files. > > On Thu, Oct 24, 2013 at 7:30 AM, Robert Willows > <robert.willows@xxxxxxxxx> wrote: >> Hi all, >> >> Thanks you Bastien and Andreas for pointing me in the right direction, >> I've worked out a protocol for getting the SSPACE tab files from a sam >> file from a MIRA assembly. >> >> Below is the commented protocol using grep and awk. >> ... > > Did you try the SSPACE provided tools/sam_bam2Tab.pl script, > http://seqanswers.com/forums/showpost.php?p=68085&postcount=135 > (included in SSPACE basic v2.0 at least)? > > It seems rather brittle - for instance it assumes for example you've > done single end read mapping so that your SAM/BAM file contains > reads with names ending in /1 and /2 (which shouldn't be there; > the read number *ought* to be in the FLAG field instead and the > read name shouldn't have a suffix at all). > > Regards, > > Peter
