User: from the mountains

Reputation:
40
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New User
Location:
United States
Last seen:
1 week, 1 day ago
Joined:
2 years, 9 months ago
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Posts by from the mountains

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Is biomaRt service down?
... I get an error like this: Error in .postForm(curl, .opts, .params, style) : embedded nul in string: '\r\n\r\n\r\n\t\r\n\tKaspersky Endpoint Security 10 for Windows\r\n\t\r\nhtml,body{height:100%}\r\n\r\nbody{width:100%;min-height:100%;margin:0;padding:0;color:#2C2C2C;font:normal 11px taho ...
written 10 days ago by from the mountains40
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cuffcompare output not including novel isoforms?
... I hope all is well. I have a quick question about my STAR -> stringtie -> cuffcompare workflow. I found it odd that there were no frags of type "j" when I typed the following: $ cut -f4 ${sample}.tracking | sort | uniq -c 3864 = 14532 c 27422 e 25872 i 801 ...
tuxedo cuffcompare rna-seq written 14 days ago by from the mountains40
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Comment: C: Is biomaRt service down?
... If that were the only issue then I would get the message that you are getting. Before this type of issue was occurring, I was getting that type of message (an empty result). I also tried other IDs and other filters and value types, and still get the same error. ...
written 16 days ago by from the mountains40
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Comment: C: Is biomaRt service down?
... Thanks for your comment. It's a good suggestion but didn't work, and I actually think my connection to the service is working, but for some reason the message shows as not connecting when I try to use certain functions. ...
written 16 days ago by from the mountains40
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Comment: C: Is biomaRt service down?
... hm. I'm running "R version 3.4.1 (2017-06-30)" which I updated only a few weeks ago (but well before biomaRt stopped working) and the biomaRt version is the same as yours. I tried doing all this on another server with the same R 3.4.1, biomaRt and BioC versions and actually got it working, but i'd l ...
written 22 days ago by from the mountains40
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Is biomaRt service down?
... Hi everyone, I am getting the following error message when I try to use biomaRt: > ensembl=useMart("ensembl") Request to BioMart web service failed. The BioMart web service you're accessing may be down. Check the following URL and see if this website is available: http://ww ...
R biomart written 22 days ago by from the mountains40
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Answer: A: RNA-seq GC content Bimodal distribution
... i see that second peak all the time with rRNA depleted libraries. rRNA depletion methods are never complete, which is reflected by the lower density peak at ~85%. You want that peak to be as low as possible. ...
written 27 days ago by from the mountains40
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Comment: C: kal's test on rpkm vs raw counts
... good to know. but why? and doesn't that seem in conflict with the formula stated in the kal's test paper? : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC25383/ ...
written 5 weeks ago by from the mountains40
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kal's test on rpkm vs raw counts
... For comparisons with 0 replicates, I am using Kal's Z-test on proportions. I am wondering, does it make more sense to run Kal's on RPKM or on raw counts, and why? I would think that RPKM is better because it is normalized by gene length. We are more interested in knowing the (transcripts_of_geneA/to ...
rna-seq written 5 weeks ago by from the mountains40 • updated 5 weeks ago by theobroma221.0k
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read orientation from library fragment
... I have been reading some literature on read orientation and unfortunately I am still confused about how read orientation relates to the original fragment. Let's say that the following is one strand of the library fragment. 5' P7 AAAAAATTTGGGGGGGGGGGG P5 3' From what I understand, before R1 is seq ...
next-gen sequencing written 4 months ago by from the mountains40 • updated 12 weeks ago by Biostar ♦♦ 20

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