extracting, stitching, converting MAF files: interval_maf_to_merged_fasta.py: command line usage?
by Anton Kratz
Dear Galaxy team / user mailing list,
my question is with respect to command line usage, not about interactive /
web-based Galaxy usage. Regarding the publication [1], section "2.3
Stitchers".
I want to use the stitcher to extract a given region from MAF files, stitch
it together and convert it to FASTA.
I downloaded and installed Galaxy according to the instructions from
http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy
I believe the actual stitcher is "interval_maf_to_merged_fasta.py" in the
/tools/maf directory (not clear from the paper or docs but I belive this is
the tool that implements this functionality).
How can I actually extract, stitch, convert with
interval_maf_to_merged_fasta.py?
I have difficulties figuring all necessary command line parameters out by
reading the source code.
F.e. here I tried to get the stiched FASTA conversion for a region defined
in "foo.bed" out of "chr1.maf":
$ python ./tools/maf/interval_maf_to_merged_fasta.py -G -i ../foo.bed -m
../chr1.maf -d hg18 -o stdout
Traceback (most recent call last):
File "./tools/maf/interval_maf_to_merged_fasta.py", line 196, in <module>
if __name__ == "__main__": __main__()
File "./tools/maf/interval_maf_to_merged_fasta.py", line 107, in __main__
if options.mafSourceType.lower() in ["cached"]:
AttributeError: 'NoneType' object has no attribute 'lower'
Is it necessary to index the MAF files first somehow? Do I have to set the
type of MAF file, and to what?
Would be great if someone could give a short overview how to stitch MAF
files command-line based.
Thank you!
Anton
References
[1] Blankenberg, D., Taylor, J., Nekrutenko, A. & Galaxy Team. Making whole
genome multiple alignments usable for biologists. *Bioinformatics (Oxford,
England)* *27*, 2426-2428 (2011)
8 years, 3 months
Error in mapping with bowtie
by Hongkyun Kim
Hi Experts!
I uploaded my data (two pair-end fasq files from illumina), processed
with fasq groomer, and then mapped processed data using a reference
genome with Bowtie.
I got strange errors I cannot possibly understand. None of the files
have ind, wped, wsf, or wpf. Any idea?
WARNING:galaxy.datatypes.registry:Error loading datatype with
extension 'ind': 'module' object has no attribute 'wsf'
WARNING:galaxy.datatypes.registry:Error loading datatype with
extension 'wped': 'module' object has no attribute 'wsf'
WARNING:galaxy.datatypes.registry:Error loading datatype with
extension 'wsf': 'module' object has no attribute 'wsf'
WARNING:galaxy.datatypes.registry:Error loading datatype with
extension 'wpf': 'module' object has no attribute 'wsf'
Thanks in advance.
8 years, 3 months
cuffdiff results missing
by i b
Hi,
I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group
one has two replicates (treated) and group two only one replicate
(untreated).
When looking at the outputs the following are empty (1 line):
TSS group FPKM tracking
TSS groups differential expression testing
CDS FPKM tracking
CDS FPKM differential expression testing
CDS overloading diffential expression testing
promoters differential expression testing
splicing differential expression testing
the other four outputs have data downloadable as excel.
Is this normal?
thanks,
ib
8 years, 3 months
quota limit
by Hongkyun Kim
Hi there,
I am a newbie at Galaxy (registered last night), and have been given
10Gb space. I wonder whether I can increase quota size somehow.
I have just uploaded two related files (each 3Gb), and then converted
one file to a new format (another 3Gb). Now, I cannot do anything.
8 years, 3 months
Galaxy intro webinar
by wlathe
Greetings all!
We will be giving a 1 hour 15 minute Intro to Galaxy webinar tomorrow (Thursday, July 19th) at 11am PDT, 2pm EDT. Registration is open and free. Registrants will also have access to a recording, slides and exercises. The webinar will go through the basics of using Galaxy, tools, histories and workflows. If you'd like to attend or would like to see more information, check our our webinar registration page: http://www.openhelix.com/cgi/webinars.cgi
Trey
(OpenHelix)
8 years, 3 months
Post
by Rachael Sirois
rsirois(a)smith.edu
8 years, 3 months
cuffcompare outputs missing
by i b
Hi,
I ran cuffcompare using 3 samples as inputs (dataset 1-2-3 cufflinks
gtf) and a reference annotation (dataset 4).
These are the outputs:
5: Cuffcompare on data 1, data 4, and others: transcript accuracy
6: Cuffcompare on data 1, data 4, and others: 1 data tmap file
7: Cuffcompare on data 1, data 4, and others: data 1 refmap file
8: Cuffcompare on data 1, data 4, and others: data 2 tmap file
9: Cuffcompare on data 1, data 4, and others: data 2 refmap file
10: Cuffcompare on data 1, data 4, and others: transcript tracking
11: Cuffcompare on data 1, data 4, and others: combined transcripts
my question:
why I don't have tmap and refmap on dataset 3?Why only 1 and 2 (arbitrary???)
Thanks,
ngs-ib
8 years, 3 months
UCSC tools
by i b
Hi,
is there a way to create a jobin my history from UCSC genome browser
that contains ONLY genes encoding for ONLY cell surface proteins?
How can I do that?
Thanks a lot!
ngs-ib
8 years, 3 months
(no subject)
by i b
ok, so if I have 3 different samples I would use 3 different goups and add
my samples as replicate within each group.
or did you mean to create just one group and add all my 3 samples as 3
replicates within that only group?
thanks a lot
ngs-ib
________________________________________
From: Jennifer Jackson [jen(a)bx.psu.edu]
Sent: Tuesday, July 17, 2012 1:58 AM
To: Irene Bassano
Cc: galaxy-user(a)lists.bx.psu.edu
Subject: Re: [galaxy-user] cuffdiff
Hello Irene,
On 7/16/12 4:11 PM, Irene Bassano wrote:
> Hi,
> just few questions about cuffdiff if anyone can answer:
>
> 1.how can I load more than two sam/bam files?Galaxy gives spaceonly for
two files
Change the tool form for the option "Perform replicate analysis:" to be
"Yes" (the default is "No"). Use two conditions (Groups).
>
> 2.what to use as input: cufflinks, cuffcompare or cuffmerge?
GTF output from any of these may be appropriate.
Please see the tutorial on Galaxy main at:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
FAQ:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
And the "Common uses" protocols on the Cufflinks web site plus their new
paper (also linked at this site, from side bar, as "Protocol"):
http://cufflinks.cbcb.umd.edu/tutorial.html
Best,
Jen
Galaxy team
>
>
> Thanks a lot!
>
> ___________________________________________________________
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--
Jennifer Jackson
http://galaxyproject.org
8 years, 3 months
