User: Delong, Zhou

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Delong, Zhou140
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Canada
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d**********@usherbrooke.ca

Posts by Delong, Zhou

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Comment: A: Reads on Y chromosome while doing sequecing with a female donor
... Hi, Thank you very much for the link and your effort! Best,   ...
written 3.4 years ago by Delong, Zhou140
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Comment: A: Reads on Y chromosome while doing sequecing with a female donor
... Hi, Thanks for your answer. I'm actually working with my local serveur via cmd line. Judging by the presence of *random.fa files in the genome I think I'm using the hg19 full version. I think I'll just remove the Y chromosome and other unwanted .fa files next time. Best,   ...
written 3.4 years ago by Delong, Zhou140
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Reads on Y chromosome while doing sequecing with a female donor
... Hello, When looking closely to my alignments data I found something interesting. Some of my reads are aligned to the Y chromosome while the sample is from a ovarian cancer cell line - in short a female donor. Indeed all of the these reads are aligned to repeated regions and for each gene on the Y ...
y chomosome paralogues rna-seq written 3.4 years ago by Delong, Zhou140
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Comment: C: Tophat2 align_summary interpretation
... 93.3% multiple alignments? That's incredibly high for me.. What is your total number of reads? What is your quality score distribution? What is your % of alignment? What is your read length distribution?   One explaination I came with is that your reads are too short to have unique alignment. Ano ...
written 3.4 years ago by Delong, Zhou140
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Comment: A: Tophat2 align_summary interpretation
... Thanks for your reply. It's assuring to know my data are good XD   I've run fastQC before tophat and it's very satisfying. The only reason I trimmed them was to be able to apply MISO (http://genes.mit.edu/burgelab/miso/docs/) afterwards. Miso demands that all reads to be the same length. A part ...
written 3.5 years ago by Delong, Zhou140
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Tophat2 align_summary interpretation
... Hello, I'm examining my tophat output data and I would like to have some opinions on my align_summary.txt. For example for one alignement I have this summary for a RNA-seq alignment. The quality score is good, and I trimmed to have fixed read lenth at 50n.   Left reads:                Input: 183 ...
multiple alignment align_summary tophat written 3.5 years ago by Delong, Zhou140 • updated 3.4 years ago by wukai1990100
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Tophat Error: Segment-Based Junction Search Failed With Err
... Hello, I don't know why I still have this problem.. I have run tophat2 with different dataset, sometimes it goes well but sometime I have this error. I run only one job at a time on a virtual machine with 8G memory without using galaxy plateform. I tried --no-coverage-search option but it changes no ...
bam samtools bowtie alignment written 4.2 years ago by Delong, Zhou140 • updated 4.2 years ago by Jennifer Hillman Jackson23k
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Comment: C: Error "Out Of Memory" When Trying To Retrieve Output
... Hello, This solved my problem. Thanks. Delong ________________________________ De : Dannon Baker [dannon.baker@gmail.com] Envoyé : 29 aoűt 2013 16:07 Ŕ : Delong, Zhou Cc : galaxy-user@bx.psu.edu Objet : Re: [galaxy-user] Error "out of memory" when trying to retrieve output Do you have debug enable ...
written 4.3 years ago by Delong, Zhou140
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Error "Out Of Memory" When Trying To Retrieve Output
... Hello, I wanted to download the accepted junction .bam file from tophat output of my local instance and I get an "out of memory" error. When I examine the server via command line, I found that a python process used by galaxy occupied more than 80% of total memory (on the virtual machine with 10G of ...
galaxy written 4.3 years ago by Delong, Zhou140 • updated 4.3 years ago by Dannon Baker270
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Comment: C: Tophat2 Not Working?
... Hi, Thanks for the feedback. Best, Delong ________________________________ De : Anto Praveen Rajkumar Rajamani [APR@hum-gen.au.dk] Envoyé : 29 aoűt 2013 14:27 Ŕ : Delong, Zhou; galaxy-user@bx.psu.edu Objet : RE: Tophat2 not working? Hi Delong, I used Tophat2 for 32 files and all worked well. I di ...
written 4.3 years ago by Delong, Zhou140

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