Dear all,
I'm trying to clip adapter sequences off the ends of my
sequencing reads. I tested the tool by purposefully adding parts of the
adapter sequence or the full adapter sequence to the 3' end. The tools is
amazing in detecting these sequences. However, I encountered some
proble
Hello, I am using the subtract (whole dataset) tool. I converted my fastq
file to tabular with 2 columns: 1. Identifier and 2. sequence. I then
"selected (a few) lines that match an expression" from this initial tabular
file and am trying to get a final dataset that is devoid of reads with the
f
Hello,
I have binned the mouse genome into fragments based on restriction
enzyme cut sites. So each bin is a fragment flanked by say BamHI. The
output file is in the interval format: chr# start and end coordinates of
each bin. I want to count how many times each bin has reads that align
Hello, I have a bed file in this format: chr# start end scores. I tried
to view it in ucsc main but it showed only where the fragments are(based on
the start and end coordinates) with numerical scores beside each fragment.
How do I view the file as a histogram format? What format will I need to
file
> extension to "bedgraph" will be enough, if not you might be required to
> enter a track line. See UCSC for details.
>
> On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong wrote:
>
>> Hello, I have a bed file in this format: chr# start end scores. I tried
>
; When I was doing this the information I used was wiggle format:
> track type = wiggle_0 name="name of track" description="description"
> useScore=1 scoreMin=0 scoreMax=6.
> ChrNo StartPos FinishPos Score
>
> Hope that makes sense/helps
> lizzy
>
>
&g
Hello, I have been using the compute function in galaxy to replace
sequences with delimiters for processing my reads. I realized that the
replace "code" in compute no longer works. Is there any other way to
replace sequences with delimiters?
Jose
_
Hi, I've been trying to use the extra DNA tool but I keep getting an error:
Traceback (most recent call last): File
"/galaxy/main/server/tools/extract/extract_genomic_dna.py", line 300, in if
__name__ == "__main__": __main__() File
"/galaxy/main/server/tools/extract/extract_genomic_dna.py", line 1
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