User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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Comment: C: Can we use CRAM files for Telomerecat?
... Sorry for the mistake. I have updated the command with sample.cram. I am using CRAM file as input instead of BAM. While converting CRAM2BAM, each BAM file is -100gb. That’s why I am not saving the intermediate BAM files. But the tool mainly uses BAM as input. https://github.com/cancerit/telomereca ...
written 3 months ago by bioinforesearchquestions280
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Can we use CRAM files for Telomerecat?
... Hi friends, I am trying to use a tool called Telomerecat for estimating telomere length. The tool takes BAM file as input. I would like to use CRAM file as input instead of BAM files. Anyone has tried it in the past using CRAM files? Because the bam files are ~ 100gb each. If I process 100-1000 ...
whole genome sequence written 3 months ago by bioinforesearchquestions280
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Comment: C: How to get differential gene expression within paired samples using EdgeR or DES
... Hi [Kevin][1] I have a very similar situation and also interested in getting the below kind of comparison for my dataset. > In order to compare, Patient51 N vs Patient51 T, what design and contrast should be selected? You are correct that the p-value comes from a 1 versus 1 comparison should ...
written 9 months ago by bioinforesearchquestions280
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Comment: C: How to Normalize the effect between group in bulk RNAseq?
... Thanks for your help, ATpoint. Sure, I will try to contact a statistician. ...
written 10 months ago by bioinforesearchquestions280
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Comment: C: How to Normalize the effect between group in bulk RNAseq?
... Hi ATpoint, I have also another kind of analysis. Total 24 samples (12samples from population1 and 12 samples from population2). I separated the pop1 samples in separate dataframe and similarly the corresponding sampleinfo to a separate dataframe. Then I used following ...
written 10 months ago by bioinforesearchquestions280
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Comment: C: How to Normalize the effect between group in bulk RNAseq?
... I have made few changes on my original post. As you mentioned I read the DESeq2 manual page 42. I have 2 populations in 4 conditions (tumor_drug,tumor alone, wt_drug, wt) as mentioned above. So I prepared the sample metadata with the below details. **Is my sample metadata in the correct format for ...
written 10 months ago by bioinforesearchquestions280
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Comment: C: How to Normalize the effect between group in bulk RNAseq?
... My collaborator gave me a list of 40 genes and asked me to do the comparisons on those genes. But I told him that I will do on the entire gene list and filter those 40 genes. Is there a way to do only on those 40 genes? For instance, some set of genes are highly expressed in both Tumor-Drug-Condit ...
written 10 months ago by bioinforesearchquestions280
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Comment: C: How to Normalize the effect between group in bulk RNAseq?
... Sure, I will update myposts. ...
written 10 months ago by bioinforesearchquestions280
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Comment: C: How to Normalize the effect between group in bulk RNAseq?
... Yes, in some of the posts, I didn't accept the answers. I thought it didn't completely address my query. Hereafter in future I will make sure of it. Thanks genomax. ...
written 10 months ago by bioinforesearchquestions280
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Comment: C: How to Normalize the effect between group in bulk RNAseq?
... First I posted this question and then I checked my previous query. Sorry genomax you people are really great in sparing your valuable time and helping us with our queries. ...
written 10 months ago by bioinforesearchquestions280

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