User: lorenzosola96

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Posts by lorenzosola96

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Comment: C: Analysis of RNA-seq data
... Thank you Albert and thank you ATpoint. Indeed my idea was to do some searches on literature in order to see house-keeping genes in different tissues and compare their expression with the expression my genes. Of course I will take in account all the paratemers you stated above. After these comments ...
written 1 day ago by lorenzosola960
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Comment: C: Analysis of RNA-seq data
... Thank you for your very precious advices. In this case I have to focus on differentially-expressed genes not on isoforms. Anyway this can be very useful for future analysis. ...
written 1 day ago by lorenzosola960
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Comment: C: Analysis of RNA-seq data
... I totally agree with you, It is not just matter to able to follow a pipeline but the most important thing is the interpretation of the results and the details of the experiment. Let's me say that if I follow correctly the most reccomended/used pipelines I will be more sure when I will analyze my res ...
written 1 day ago by lorenzosola960
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Comment: C: Analysis of RNA-seq data
... Thank you again very clear indeed if the fold changes will be very close to zero it will mean no expression right? So we can filter these genes because are basically they are not expressed. ...
written 1 day ago by lorenzosola960
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Comment: C: Analysis of RNA-seq data
... Indeed I really appreciate your suggestions especially the second one. So basically txt import takes the output from Salmon (transcript level abundances) and transform this to the gene level to perform Differential Expression Analysis right? ...
written 1 day ago by lorenzosola960
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Comment: C: Analysis of RNA-seq data
... Thank you your suggestion is greatly appreciate and it is exactly what I waiting for. So if I understood right now I did qualitative evaluation in the right way. Now to do a quantitative assessment I have to proceed with DESeq2 (DEA) right? Instead talking only about TPM how can I set up a cut off t ...
written 1 day ago by lorenzosola960
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Comment: C: Analysis of RNA-seq data
... Thank you for you suggestion. Actually I’m reading and following that pipeline. I’m not sure you replied exactly to my questions. I did this post to have ideas/feedbacks about my work and to know if I understood correctly that manual. Considering what I wrote, I’m right or wrong? Thank you again! ...
written 1 day ago by lorenzosola960
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Analysis of RNA-seq data
... Hi to all, I have RNA-seq data from 31 tissues of 2 different individuals. My goal is to evaluate the expression of various genes of interest and to compare the expression level among these tissues. I read throughout a lot of papers and posts and I tried to set up my pipeline. I mean first of all a ...
rna-seq written 2 days ago by lorenzosola960 • updated 1 day ago by Istvan Albert ♦♦ 85k
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Normalization with deepTools
... Good morning, I'm doing RNA-seq analysis. I have .bam files coming from 31 different tissues. My goal is to normalize these data in order to obtain .bigwig files and compare them on IGV. Can I use bamCoverage (from deepTools) to do that? If yes, how can I do it? Thank you in advance for your time ...
rna-seq written 7 days ago by lorenzosola960 • updated 7 days ago by Friederike6.5k
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Comment: C: Suggestion for Differential Expression analysis
... Ok thank you actually I have the same type of tissues from another individual so I can do it to determine the biological relevance. Now I have to improve my skills on R to do it. Thank you again! ...
written 12 days ago by lorenzosola960

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