I have a problem converting paired reads with paired end reads from
ABi, in the color code the reads started with a G and afterwards with
numbers instead of T02102103... , so I guess the program assumes the T
as hardcoded instead of using the G as last base
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I have been successful by using the online tool to align Illumina pair end
reads , each direction 5GB, and also generated a pileup of 680,000,000
but the filtering of the pileup always fails, it runs for several hours and
I get an empty file back. I tried different options and different pileups,
always the same.
Could somebody please help or what is the trick?
Dear Sir or Madam,
I am planning to do clustering of several libraries based on the output of cuffcompare or cuffdiff, as they allow me to construct a matrix whose columns represent the libraries and rows are the count of transcripts or genes. I want to construct the matrix because it is the required input format of many RNA-seq clustering softwares, e.g. baySeq, HTSCluster. However, by reading the answer of question "I want to find differentially expressed genes. Can I use Cufflinks in conjunction with count-based differential expression packages?" in the cufflinks FAQ list, it is suggested not to convert FPKM value to count data.
Now my question is
1. It seems that it is better to run everything up to cuffdiff, but does cuffdiff allow multiple sample comparison because I read somewhere that even for multi-samples it still compare tham pairwisely? In a sense, because I want to do clustering which needs some quantitative data source to do the merging, will cuffdiff provide me some quantitative measures rather than the test score and p-value which is too qualitative to include?
2. If I really need to get count data from the FPKM values, how do I obtain the mentioned "effective length"? Would it be better if I treat each assembled transcript as an object in clustering, rather than genes. What does it mean "you'd be throwing away Cufflinks' uncertainty" even with using isoforms as objects? How should I include the uncertainty into my clustering?
I ran into this error running cuffdiff. I had a hard time debugging
this user error, so I though it would be nice to share the solution.
This was in a local instance, but I don't see why it wouldn't happen
in Galaxy Main under the same circumstances.
Tool execution generated the following error message:
Error running cuffdiff. Error: cannot open reference GTF file
CONDITION,CONTROL for reading
The tool produced the following additional output:
cuffdiff v1.3.0 ()
cuffdiff --no-update-check -q -p 4 -c 1000 --FDR 0.050000 -N -b
The problem ended being the use of "Perform Bias Correction"(-b) and a
GTF file with no "Database/Build" associated. Looking at cuffdiff
wrapper I found, if a FASTA reference is not selected from the
history, the FASTA reference of the GTF file associated build is used.
If there is not build association, your cuffdiff run will fail with
this not so helpful error.
My feeling is, cuffdiff should check for a non-dashed string after
'-b' and complain if is absents, but this doesn't happen currently.
I have downloaded and installed a local instance of galaxy on the linux
server using my user account according to here:
Then I ran the following command:
> sh run.sh
and accessed galaxy through the local firefox browser on the server
Now I am trying to use some NGS files for FASTQ Groomer. Each file is in
the server disk already, but very large (~8G each).
I was not able to use the "upload file from your computer" function under
the "Get Data" tab (maybe because each file is too large).
What am I supposed to do?
> I have downloaded and installed a local instance of galaxy on the linux
> server using my user account according to here:
> I then created a library and linked some datasets on the local server.
Then I ran FastQ Groomer on some datasets.
The results were shown under "History".
I am wondering whether the results were saved automatically somewhere
on the local server? If so, what is the default path?
i have added a tool to the galaxy
and it is showing me the desired result on history panel when I execute, now i
have added another tool and i want to show its result on the same file which
was the output of my first tool . here is the relative code of both python and xml file
bpup = sys.argv
bpdwn = sys.argv
userid = sys.argv
output_name = sys.argv
out = open( output_name, 'w' )
<command interpreter="python">mytool.py $bpup $bpdwn $userid $out_file1</command>
<input> some inputs
<data format="txt" name="out_file1" />
I am trying to fetch multiple column from a table here is my code
for row in result_set:
db += [(row ['chr'],str(row[ 'user_id' ]), False),]
i want to concatenate 'start' column and 'end' column with this output , how can i do that