User: top5

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top510
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Posts by top5

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Comment: C: Determination of target genes of DE miRNAs and interpretation of the sequencs?
... Now i understand what do you mean, yes you are right i will try it now !! Thank you so much. I didn't think in the first place. ...
written 17 days ago by top510
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Comment: C: Determination of target genes of DE miRNAs and interpretation of the sequencs?
... Yes i could do that but miRanda gives target sequences of genes. My main question is, after I got the target sequences, I used blastn to find out which genes these sequences belong to, is this the correct way? Or do you know another packages to do that? Because i have lack of information about it ob ...
written 17 days ago by top510
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Comment: C: Determination of target genes of DE miRNAs and interpretation of the sequencs?
... Thank you so much your answer but my species is rabbit that is why i used miranda to scan its reference genome, the package that you suggest does not include this species... ...
written 17 days ago by top510
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Determination of target genes of DE miRNAs and interpretation of the sequencs?
... Hello, I recently worked on predicting target sites of DE miRNAs by using miranda v3.3a but i get just ref sequences and alignment score etc. Then i used 'blastn' to find which genes are aligned for the ref sequences that i found in miRanda. But do you think i did right way? I do not want to do som ...
gene alignment sequence rna-seq written 23 days ago by top510 • updated 22 days ago by Kevin Blighe60k
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Comment: C: Why the evalues are different from online blast when using blastn -remote option
... I am using same version both but thank you for the tip i'll try to mimick all the settings. Yes the evalue that i gave is pointless but it also turned significant evalues to meaningless. ...
written 4 weeks ago by top510
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Comment: C: Why the evalues are different from online blast when using blastn -remote option
... Thank you for the note :) ...
written 4 weeks ago by top510
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Why the evalues are different from online blast when using blastn -remote option
... Hello, I am using blastn -remote option in terminal. But the results of evalues are different from online. In remote option evalues are approximately 3 times bigger than the online results. For example in online blast the result of e value 4.4 but in terminal by using remote option it is 12. The c ...
remote blastn blast written 4 weeks ago by top510 • updated 4 weeks ago by lieven.sterck7.9k
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Comment: C: How to find mirna target genes of oryctolagus cuniculus?
... Thank you so much, i will definitely try it. ...
written 8 weeks ago by top510
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Comment: C: How to find mirna target genes of oryctolagus cuniculus?
... i think it is not working or i could not find the way , actually i just want to find prediction. i would be appreciate if you could help me about it... ...
written 8 weeks ago by top510
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How to find mirna target genes?
... Hello, I have DE miRNAs and i am trying to find target genes and i couldn't find a R package by using reference genome the most of the packages take species from tools that is already online. Could you please help me about it? ...
gene R next-gen rna-seq written 8 weeks ago by top510

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