User: Martombo

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Martombo2.6k
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Posts by Martombo

<prev • 308 results • page 2 of 31 • next >
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Comment: C: Iteration to count the number of raw reads
... your use of ` is messing up this line: `gunzip -c $f1 | echo $((`wc -l`/4))` ...
written 6 months ago by Martombo2.6k
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Comment: C: Is Ingenuity Pathway Analysis still relevant for analyzing RNA-seq data?
... has it ever been? ...
written 6 months ago by Martombo2.6k
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Comment: C: Deseq2 positive results for genes highly variable between replicates
... In my experience, this kind of result typically stems from the presence of a very high variability in samples of the same group (compared to between groups). You may want to correct for possible co-variates in your data (see svaseq) or simply filter out results with high dispersion. ...
written 7 months ago by Martombo2.6k
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Comment: C: Error in some hog codes using pyham
... this is the best name for a package in the history of bioinformatics! ...
written 7 months ago by Martombo2.6k
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Comment: C: Removing adaptors from smallRNA seq data
... well it does seem like 60% of reads were trimmed, right? ...
written 7 months ago by Martombo2.6k
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Comment: C: Removing adaptors from smallRNA seq data
... Do a multiple sequence alignment of the last ~15 nucleotides of some hundred of reads and you should be able to identify the sequence of your adapter ...
written 7 months ago by Martombo2.6k
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Comment: C: Selecting the consensus/overlapped genes from the DE study
... As they state in the paper you linked, it is expected that by taking the overlap of different tools you improve the absolute accuracy measures. As I mentioned in my original comment, you will select genes whose differential expression is simply more significant. You can however also do that by lower ...
written 7 months ago by Martombo2.6k
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Comment: C: Finding the best combination of covarites in a multivariate linear regression
... Are the numbers of genes / patients you mention as examples the ones you are actually working with? It is a bit hard to understand from your question. In that case, I would use some machine learning to select features if needed (lasso) and model the explanatory variable of OS (random tree). ...
written 8 months ago by Martombo2.6k
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Comment: C: how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
... I think you can definitely use ESTIMATE with RNA-seq data as this was done by the authors themselves. See the tool's [website][1]. [1]: https://bioinformatics.mdanderson.org/estimate/index.html ...
written 8 months ago by Martombo2.6k
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Comment: C: Question about differentially expressed genes selection for low sample size data
... I think you can talk about a "trend" in this case, but additional validation is needed. ...
written 8 months ago by Martombo2.6k

Latest awards to Martombo

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 4 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Scholar 6 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Epic Question 11 months ago, created a question with more than 10,000 views. For Sjdboverhang Option In Star
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Student 14 months ago, asked a question with at least 3 up-votes. For Sjdboverhang Option In Star
Popular Question 15 months ago, created a question with more than 1,000 views. For human Natural Antisense Transcript database
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 23 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Scholar 24 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 2.0 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Scholar 2.2 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Great Question 2.7 years ago, created a question with more than 5,000 views. For Sjdboverhang Option In Star
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