User: Xianrong Wong

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Posts by Xianrong Wong

<prev • 11 results • page 1 of 2 • next >
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bedtools, changing output attributes
... Hi, I'm using the bedtools "Intersect intervals find overlapping intervals in various ways" tool. I used it in a workflow and am trying to (1) change the output filename and data-type, (2) only show the output (with the name changed) and (3) use (2) as an input to another tool in the workflow. The ...
bedtools written 23 months ago by Xianrong Wong90
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bowtie1 missing built-in genome indices
... Hi, I need to install bowtie1 for some reason.  I installed package_bowtie_0_12_7 and bowtie_wrappers.  The tool displays well on galaxy but it's missing the built in genome indices for mapping.  How would I rectify this issue?  Thanks in advance!     ...
bowtie1 built-in index written 2.0 years ago by Xianrong Wong90 • updated 2.0 years ago by Jennifer Hillman Jackson24k
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Correctly installing to toolshed
... Hi, I'm new to publishing tools/repository on the toolshed.  I have used planemo and lint and tests as well as serve all worked.  I was able to use the tool.  However, when I uploaded it onto the test tool shed and imported the tool on a cloud instance, I keep getting this error when running job: F ...
toolshed written 2.0 years ago by Xianrong Wong90 • updated 24 months ago by Dave B.410
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Answer: A: Read Simulator
... 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 11 ...
written 4.0 years ago by Xianrong Wong90
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Replace Function On Galaxy
... 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 ...
galaxy written 4.4 years ago by Xianrong Wong90 • updated 4.4 years ago by Jennifer Hillman Jackson24k
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Comment: C: Displaying Bed Files In Ucsc
... Thank you for the advise. I am able to view now when I use track type=wiggle_0 but I can only do it a few chr at a time which is good enough. Just curious, what track type do I type in when I want it to be bedgraph? It seems the _0 was important for wiggle. Jose ...
written 5.8 years ago by Xianrong Wong90
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Comment: C: Displaying Bed Files In Ucsc
... I changed it to bedgraph and can no longer view in UCSC (the button to view in UCSC was not there anymore). I had it in bed format subsequently and put in a header. I was looking at the bedgraph/wiggle header documentation on UCSC but don't find any that describes displaying scores in histogram fo ...
written 5.8 years ago by Xianrong Wong90
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Displaying Bed Files In Ucsc
... 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 ...
written 5.8 years ago by Xianrong Wong90 • updated 5.8 years ago by Jim Robinson150
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Operate On Genomic Intervals
... 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 to ...
bowtie alignment written 5.8 years ago by Xianrong Wong90 • updated 5.8 years ago by Jennifer Hillman Jackson24k
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Subtract
... 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 fe ...
written 5.8 years ago by Xianrong Wong90 • updated 5.8 years ago by Jennifer Hillman Jackson24k

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