I am trying to join two groomed fastq files from a paired-end Illumina
read using the fastq joiner tool. The drop-down menus correctly
identify the groomed fastq files, but after cranking for a few minutes
the tool produces empty output:
"FASTQ joiner on data 5 and data 4
empty
format: fastqsanger,
>
> Brand new galaxy user here.
>
> I ran an RNA-seq Illumina experiment in which I compare cells from wild
> type animals and cells from animals that have a deletion in a splicing
> factor. Now I have my data in fastq format and need to do analysis to
> figure out which transcripts are changed and
Hello Jinhai YU,
The error indicates that there was a problem with the BAM file/index.
When you loaded the larger file into Galaxy, did you use FTP? Was it
successful? Using a utility would allow you to track the progress, if
you are not certain. An incomplete load could generate an error like
Hello,
Apologies for the delay in reply. We wanted to point you to the
documentation for the tool and the author's help email:
Doc:
http://cufflinks.cbcb.umd.edu/index.html
Email:
tophat.cuffli...@gmail.com
They also have a mailing list (the link is on the right menu bar of
their web page).
Hello,
I using operate on genomic intervals on some data and it always seems
to ignore the strand information. Am I missing something or does "operate of
genomic intervals" disregard strand information? Is there a tool that does the
inner join function and takes into account strand in
Hi,
I want to use cufflinks handle the results of Tophat. Cufflinks uses FPKM to
normalize the expression data. I think FPKM is for pair-end reads. right? My
reads are single-end. Is it right if I use FPKM?
Thank you very much!
Victor
___
Hello,
The Galaxy instance for LEfSe is run by another group. If you haven't
done so already, it might be best to contact them directly to see what
their suggestions are. The contact link is on the home page, in the
middle pane, last sentence:
http://huttenhower.org/galaxy/
Hopefully they wi
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