Hi Galaxy, Can you please enlighten me on the concept of MAF alignments ? Are they the same as BLASTZ searches ???? Thanks . Amit.
On Nov 25, 2010, at 9:20 AM, pande wrote:
Can you please enlighten me on the concept of MAF alignments ? Are they the same as BLASTZ searches ????
The short answer is that MAF is just a file format for reporting local alignments of 2 or more sequences: http://genome.ucsc.edu/FAQ/FAQformat#format5 A longer answer is that MAF is the format by which UCSC reports their many-species alignments, such as the 46-species alignment referred to here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=157689212&c=chr21&g=cons46way BLASTZ doesn't produce MAF as output, and it is only a pairwise aligner. However, it is (actually, was) a piece of the MULTIZ package which combines pairwise alignments into a multiple alignment and does produce MAF. Hope that helps, Bob H P.S. BLASTZ is considered obsolete, and has been replaced by LASTZ. http://www.bx.psu.edu/miller_lab http://www.bx.psu.edu/~rsharris/lastz
On Nov 25, 2010, at 9:20 AM, pande wrote:
Can you please enlighten me on the concept of MAF alignments ? Are they the same as BLASTZ searches ????
and on Nov 25, 2010, at 9:33 AM, Bob Harris replied:
The short answer is that MAF is just a file format for reporting local alignments of 2 or more sequences: http://genome.ucsc.edu/FAQ/FAQformat#format5 [[ more, snipped ]]
It turns out there's another format with the same name, MAF, as part of the MIRA sequence assembler project. This is completely unrelated to UCSC MAF. See http://mira-assembler.sourceforge.net/docs/chap_maf_part.html Looking at that description it seems to fit the general idea of SAM, i.e. it's a short-read-focused format that allows a read mapper to convey information to an assembler. Now, I'm sure the original poster was asking about UCSC MAF, not MIRA MAF, but the galaxy team should be aware that there are two different things called MAF in this field. Bob H
Hi all, I hope you can help. I'm trying to load illumina sequencing data on Galaxy throu the upload data function. But the data never completes loading. can someone help? Thanks On 30 Nov 2010, at 15:54, Bob Harris wrote:
On Nov 25, 2010, at 9:20 AM, pande wrote:
Can you please enlighten me on the concept of MAF alignments ? Are they the same as BLASTZ searches ????
and on Nov 25, 2010, at 9:33 AM, Bob Harris replied:
The short answer is that MAF is just a file format for reporting local alignments of 2 or more sequences: http://genome.ucsc.edu/FAQ/FAQformat#format5 [[ more, snipped ]]
It turns out there's another format with the same name, MAF, as part of the MIRA sequence assembler project. This is completely unrelated to UCSC MAF. See http://mira-assembler.sourceforge.net/docs/chap_maf_part.html Looking at that description it seems to fit the general idea of SAM, i.e. it's a short-read-focused format that allows a read mapper to convey information to an assembler.
Now, I'm sure the original poster was asking about UCSC MAF, not MIRA MAF, but the galaxy team should be aware that there are two different things called MAF in this field.
Bob H _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
On Wed, Dec 1, 2010 at 11:49 AM, Emmanouil Metzakopian <emetzak@nimr.mrc.ac.uk> wrote:
Hi all,
I hope you can help. I'm trying to load illumina sequencing data on Galaxy throu the upload data function. But the data never completes loading. can someone help?
Thanks
That has nothing to do with MAF - did you reply to the wrong thread? Peter
Hi all, I hope you can help. I'm trying to load illumina sequencing data on Galaxy through the upload data function. But the data never completes loading. can someone help? Thanks
Hi Emmanouil what you can try doing is, putting your illumina read data( whats the size) on a ftp server and giving the ftp address of the dataset, to upload best Abhay On 1 December 2010 13:04, Emmanouil Metzakopian <emetzak@nimr.mrc.ac.uk>wrote:
Hi all,
I hope you can help. I'm trying to load illumina sequencing data on Galaxy through the upload data function. But the data never completes loading. can someone help?
Thanks
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participants (5)
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Abhay Krishna -
Bob Harris -
Emmanouil Metzakopian -
pande -
Peter