Can anyone get SHORE/SHOREmap to work with CASAVA 1.8 (Illumina Hi chemistry v3)? If so could they offer some tips?
My details follow:
I have a lane of arabidopsis 2x100 (PE) sequence and am running SHORE/SHOREmap for the first time.
For the uninitiated, SHORE appears to be a general purpose NGS mapping pipeline capable of deploying a number of mapping engines, though it appears to prefer "genomemapper", for a number of different analysis tasks. SHOREmap is a visualization/analysis tool requiring, more or less, SHORE input.
The first part seems good:
SHORE v0.6.2beta (rev. c5f8-1879) pulls in the fastq files and aligns them to a TAIR9 fasta reference with genomemapper0.4.3. The PE correction and "merging" appear to go fine.
The problems start when I attempt to generate the homozygous_snp.txt file needed by SHOREmap to continue. Earlier versions of SHORE would have "shore consensus" run to do this. But:
(1) shore consensus with v0.6.2beta has a mysterious, new parameter, "-g" that I don't know how to set. This one:
so attempts to run consensus produce no joy.
(2) SHORE v0.6.2beta documentation recommends using "qvar" instead of consensus. Running qvar produces a gigantic (37G) "pileup.txt" file and, with some parameter settings, generates CNV info. But the homozygous_snps.txt file is always zero length.
(3) SHORE v0.5 "shore consensus" would be my second choice. But "shore import" chokes on the new CASAVA 1.8 header info (you know, the abandonment of the /1 and /2 fields?). So again: brick wall.
I don't see a forum or email list devoted to these programs. I emailed one of the authors, Stephan Ossowski, earlier this week. But no response so far.
Any advice?
--
Phillip
My details follow:
I have a lane of arabidopsis 2x100 (PE) sequence and am running SHORE/SHOREmap for the first time.
For the uninitiated, SHORE appears to be a general purpose NGS mapping pipeline capable of deploying a number of mapping engines, though it appears to prefer "genomemapper", for a number of different analysis tasks. SHOREmap is a visualization/analysis tool requiring, more or less, SHORE input.
The first part seems good:
SHORE v0.6.2beta (rev. c5f8-1879) pulls in the fastq files and aligns them to a TAIR9 fasta reference with genomemapper0.4.3. The PE correction and "merging" appear to go fine.
The problems start when I attempt to generate the homozygous_snp.txt file needed by SHOREmap to continue. Earlier versions of SHORE would have "shore consensus" run to do this. But:
(1) shore consensus with v0.6.2beta has a mysterious, new parameter, "-g" that I don't know how to set. This one:
Code:
-g INT Core offset - do not trust the first and last -g positions of the alignment. default: max MM's
(2) SHORE v0.6.2beta documentation recommends using "qvar" instead of consensus. Running qvar produces a gigantic (37G) "pileup.txt" file and, with some parameter settings, generates CNV info. But the homozygous_snps.txt file is always zero length.
(3) SHORE v0.5 "shore consensus" would be my second choice. But "shore import" chokes on the new CASAVA 1.8 header info (you know, the abandonment of the /1 and /2 fields?). So again: brick wall.
I don't see a forum or email list devoted to these programs. I emailed one of the authors, Stephan Ossowski, earlier this week. But no response so far.
Any advice?
--
Phillip
