User: eva.pinatel

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eva.pinatel10
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New User
Location:
Italy
Last seen:
5 months, 1 week ago
Joined:
4 years, 5 months ago
Email:
e**********@itb.cnr.it

Posts by eva.pinatel

<prev • 6 results • page 1 of 1 • next >
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referencePrepare function in IntEREst package
... Hi everyone, I'm trying to use referencePrepare function in IntEREst package on a mouse gtf file downloaded from gencode doing this: Mouse_ref<- referencePrepare (sourceBuild="file", filePath="gencode.vM19.primary_assembly.annotation.gtf",collapseExons=TRUE,fileFormat="gtf",annotateGen ...
intron retention interest package written 5 months ago by eva.pinatel10
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Answer: A: derfinder on bacteria PE strand specific RNA-seq
... Hi Leonardo, thank you for the quick reply. I' will try to go on with the analysis and let you know if I have problems with annotation files. Best regards Eva ...
written 2.6 years ago by eva.pinatel10
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derfinder on bacteria PE strand specific RNA-seq
... Hello, I'm trying to analyze a set of bacterial, paired-end, strand specific RNA-seq with derfinder (if it is possible). I see some major points I would like to have some suggestions about: 1)My data are strand specific and derfinder doesn't seem to consider this option, it is correct to perform t ...
derfinder written 2.6 years ago by eva.pinatel10
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Diffbind discordant "Called" column in the output when setting filter parameter in dba.count
... Dear dr. Stark and community, I'm using Diffbind to obtain differential expression values for a series of interesting regions and I have some questions.I run the following: TF1_initial_IP=dba(sampleSheet="TF1DiffBind_optimal02_IP.csv",config=data.frame(fragmentSize=130), peakCaller="narrow",bCorP ...
normalization diffbind written 4.1 years ago by eva.pinatel10 • updated 4.1 years ago by Rory Stark2.8k
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Answer: A: dba.analyze settings having deeper input than ChIP
... Hi Rory, Thank you for clarification and quick reply. >To check I understand correctly, you have a total of six (6) ChIP samples, correct? Two each of three condition/treatments (WT-stim, WT-unstim, KO-stim). You also have six corresponding Input samples, correct? Yes, you are correct. As in b ...
written 4.4 years ago by eva.pinatel10
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dba.analyze settings having deeper input than ChIP
... Dear Dr Stark, I have maybe a naïve question about dba.analyze function. My experiment consist in: WT-stimulated WT-unstimulated(few leaky binding) KO-stimulated (negative control) immuno-precipitated samples, each performed in duplicate with its own input on a small bacterial g ...
diffbind written 4.4 years ago by eva.pinatel10

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