Re: [galaxy-user] about Mapping Quality

[Jeremy Goecks]

Tophat/Bowtie does not yield mapping quality, so, as per the SAM spec, that 
field is set to 255, indicating that quality is unavailable.

http://samtools.sourceforge.net/SAM1.pdf

Best,
J.

On Feb 7, 2012, at 5:46 PM, Li, Jilong (MU-Student) wrote:

> Hi all,
> 
> I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file, the 
> value of some mapping quality (the 5th column) is 255. What does it mean? And 
> I found these reads which have mapping quality 255 mapped to unique place.
> 
> Thanks!
> 
> Victor
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[galaxy-user] about Mapping Quality

[Li, Jilong (MU-Student)]

Hi all,

I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file, the 
value of some mapping quality (the 5th column) is 255. What does it mean? And I 
found these reads which have mapping quality 255 mapped to unique place.

Thanks!

Victor
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Re: [galaxy-user] How can I tell what programs are used by a tool?

[Peter Cock]

On Tue, Feb 7, 2012 at 9:52 PM, Beale, Holly (NIH/NHGRI) [F]
 wrote:
> Hi all --
>
> I'd like to know what programs are used when I run a tool on my data.
> Ideally I'd also like to know what parameters are passed to command
> line tools.

The short answer is you can't, other than by reading the tool's
documentation (ideally within Galaxy below the options), and/or
reading the tool's source code (the XML file plus any scripts).

Some Galaxy tools are simple wrappers for a single command
line tool, in which case it is usually clear how the parameters
offered to you in the Galaxy interface translate to matching
command line arguments. Such Galaxy tools should make
this clear in their documentation, along with giving you clear
citation information for the underlying tools.

Other Galaxy tools are complex scripts/tools that may call
several other command line tools internally

So it depends.

Peter
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[galaxy-user] How can I tell what programs are used by a tool?

[Beale, Holly (NIH/NHGRI) [F]]

Hi all --

I'd like to know what programs are used when I run a tool on my data. Ideally 
I'd also like to know what parameters are passed to command line tools. 

For example, I uploaded a sam file to the main galaxy server at PSU. I ran 
Filter Indels. I got output. What programs were used in this manipulation? 
samtools mpileup? GATK? FASTX toolkit?

I hope I'm missing something extremely obvious. 

Thanks for your help.

Holly


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Re: [galaxy-user] Question about uploading custom index for bowtie

[Jennifer Jackson]

Hi William,

To be sure that we are talking about the same thing, you are trying to 
use a custom reference genome with Bowtie? As the target genome? If so, 
then what you want to load is a fasta file of the 
chromosomes/scaffolds/contigs that represent that species, for a 
particular genome build. This may come from a public source or from your 
own project, if you are assembling a genome. But regardless of source, 
the final product should be a fasta file, which you load into a history 
and label as fasta, and that is what Galaxy would accept as a valid 
custom reference genome input on tool forms.


If all of this sounds like what you are wanting to do, then I am not 
clear where the fastq data fits in. The query in a Bowtie job would be 
in fastq format, but no indexes are needed for a query. Indexes should 
never be datasets in a history.


Now, if you are doing something different, such setting up databases in 
a local install, then creating indexes would be part of that process, 
but the Galaxy UI is not the place to this. Instead, you will want to 
follow the procedure in this wiki: 
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (in particular, see 
"Setting Up the Reference Genomes for NGS Tools")


All of that said, there are no specific blocks that would prevent you 
from using something other than a full reference genome as a target in a 
Bowtie run. I am fairly certain that almost any properly formatted fasta 
file could be used as long as the sequence identifiers were unique 
within the file. I've created and used small "dummy" fasta files as 
custom reference genomes with Bowtie myself without issues.


My apologies if your question is still not addressed. So if this does 
not clear things up, maybe it would help if you explained a bit more 
about what the final goal is? We want to make sure you are getting the 
correct help to resolve any outstanding issues,


Best,

Jen
Galaxy team

On 2/7/12 12:34 PM, William Light wrote:

Jennifer,

I am having some issues figuring out if I can use bowtie to take my
index (I have two that I want to upload) and generate one fasta file.
  When I use the bowtie-inspect command, the only thing I seem able to
generate is a list of the sequences used to make the index (which are
SOLiD sequences that I used to make the index) rather than one fasta
file that represents the seqeunce.  I have the fastq that I used to
generate the reference uploaded right now, and in poking around, it
seems that there is some issue with making the .ebwt files on a platform
other than the one that galaxy runs on.  Am I just missing the right
command line settings for making one fasta file?

  - Will Light
Northwester University

On Mon, Feb 6, 2012 at 8:14 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote:

Hello William,

To use a custom reference genome, all you need to upload is the
single fasta file for the genome. Galaxy will do the rest and create
indexes as appropriate.

Hopefully this helps!

Thanks,
Jen
Galaxy team


On 2/6/12 11:51 AM, William Light wrote:

I recently tried to upload a custom made index for bowtie using
Filezilla as my FTP source, but I got an error message, I think
due to
the autodetect for file type not recognizing this file type.  Is
there
something special that I should do to upload my six .ebwt files
for my
reference?



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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/__Support





--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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Re: [galaxy-user] SamTools Filter Pileup "Only report variants?" option is misleading

[Jennifer Jackson]

Hi Jesse,

We agree that the original "pileup" tool does not have all of the 
functionality that one might want. The tool authors seem to also agree, 
and developed an upgraded version called "mpileup". This has recently 
been wrapped and added to the Galaxy main public instance in the same 
'NGS: SAM Tools' tool group.


The 'MPileup SNP and indel caller' tool form has a summary of the 
available options and links to the full documentation, including the 
SAMTools' authors and support/discussion groups.


Thanks for the feedback and hopefully you will find the Mpileup tool 
useful and/or SAMTools discussion groups a helpful resource,


Best,

Jen
Galaxy team

On 1/26/12 8:38 AM, Jesse Erdmann wrote:

In using the filter pileup tool we've discovered that the option "Only
report variants?" will throw away lines that have indels provided that
they do not contain any SNPs.  For example the line:

chr188427041C   38
..+1A..+1A.+1A.,..+1A.,.+1A,.,..,...,^~.^~,^~,^~,
HFEHBFHHBFHHHEHHHAHHHFHG#E

will not be included in the filtered results.  At the very least we
would recommend relabeling the option to "Only report SNP variants?"
But it would also be helpful to include an option to filter for both
SNP and indel variants.  Thanks!



--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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