User: stijn.vandenbrande

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Posts by stijn.vandenbrande

<prev • 8 results • page 1 of 1 • next >
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Comment: C: miRanda output meaning?
... Hi, No, I'm currently still using miRanda but I might complement it by using other Tools. Anyway, if you do not use the default parameters and therefore add this function " -strict " in the command, this means that you require strict alignment in the seed region (position 2-8). We already identifie ...
written 2.1 years ago by stijn.vandenbrande30
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Reverse complement transcripts in a TSA?
... Hi all, When looking for potential miRNA binding sites against a TSA available on NCBI, we blast the transcript hits to NCBI. It appears that sometimes, the transcript of the TSA is actually the reverse complement of the mRNA on NCBI. Is this normal? And how is this possible? Thanks Cheers ...
tsa reverse complement rna-seq written 2.1 years ago by stijn.vandenbrande30
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Comment: C: miRanda only displays hits?
... Thanks! How should I command this in terminal? If i run miranda: file1 file2 and then add "grep -A 1 "Scores for this hit:" rad.txt | sort | grep >", it gives an error? ...
written 2.5 years ago by stijn.vandenbrande30
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miRanda only displays hits?
... Hi, Is it possible that the output file of miranda only displays hits, without also displaying all those where no hits were found? ...
rna-seq written 2.5 years ago by stijn.vandenbrande30
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Comment: C: miRanda output meaning?
... Interesting research! I'll go through the article when I have some time and might change from miRanda to another tool. Sure, good idea ...
written 2.5 years ago by stijn.vandenbrande30
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Comment: C: miRanda output meaning?
... Thank you for the fast reply. I didn't do miRanda analysis on the miRNAs of interest, I'm rather just learning how to interpret the result using the examples (which were present in the miRanda download). I will go through the article, but do you have a better alternative then miRanda for miRNA targe ...
written 2.5 years ago by stijn.vandenbrande30
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miRanda output meaning?
... Hello, After using the miRanda tool the first time, I've got output like this: **Score: 167.000000 Q:2 to 20 R:3340 to 3360 Align Len (18) (83.33%) (94.44%)** Could someone tell me how to interpret? Is the "score" the miRSVR score? But then what does all the rest mean? Many thanks! ...
rna-seq written 2.5 years ago by stijn.vandenbrande30 • updated 2.5 years ago by WouterDeCoster42k
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how to install & run miRanda
... Hello, I have no experience what so ever regarding bio-informatics. Now, for my research, I would like to do microRNA target predictions using the miRanda tool. Now, linux was installed on my PC and I've been able to compile the miRanda tool (I guess) in Terminal. But how do you run/install it?? M ...
rna-seq written 2.5 years ago by stijn.vandenbrande30 • updated 2.3 years ago by Biostar ♦♦ 20

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