User: Martombo

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Martombo2.6k
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Posts by Martombo

<prev • 308 results • page 1 of 31 • next >
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Answer: C: Interpretation problem at PCA plot for detecting batch effect
... There are better ways to assess the presence of batch effects. First thing, FPKM is not a robust normalization method to compare different samples. Use the normalization methods of R packages like DESeq2 or limma-voom, it would then be more appropriate to look for a batch effect. You could also remo ...
written 8 days ago by Martombo2.6k
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Comment: C: predicting 3D structure of protein from DNA sequence
... I assume you have cDNA that can be easily translated to protein sequence? If so, you can perform an analysis called homology modelling. [Swiss-model][1] is an example of a simple tool that can do that. [1]: https://swissmodel.expasy.org ...
written 13 days ago by Martombo2.6k
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Comment: C: Maths implications: log2 transformation before or after normalisation
... Well it depends on the normalization, if it's quantile normalization it should not make a difference if you log transform before or after, provided you don't have negative numbers. ...
written 4 weeks ago by Martombo2.6k
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Answer: C: Bioinformatician, a jack of all trades, but in the eye of the CV-beholder a mast
... I believe there is generally some misconception about the amount of previous knowledge and technical skills that is expected from new employees. In every job, even the most competent person still needs to learn a lot. So the ability to learn and adapt to a new position is much more valuable. This is ...
written 7 weeks ago by Martombo2.6k
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Comment: C: gene_bodyCoverage.py No usable output...why?
... Alright, are you using bash? If so you can run an awk one liner to get the 12 column you need. Something along these lines should work: awk 'BEGIN{OFS="\t"}{$7=$2; $8=$3; $9="0,0,0"; $10=1; $11=$3-$2","; $12="0,"; print}' ...
written 10 weeks ago by Martombo2.6k
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Comment: C: gene_bodyCoverage.py No usable output...why?
... And yet, here we are ;) Just a general tip for bioinformatics: always check the results you get, you cannot simply trust any program blindly. Even popular formats like BED, GTF can have slightly different properties / requirements depending on the tool you are using. The error is telling you that t ...
written 10 weeks ago by Martombo2.6k
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Comment: C: gene_bodyCoverage.py No usable output...why?
... well your input file doesn't fit the required BED format, check it out [here][1]. Also, if I remember correctly, the program requires tab-separated input. [1]: https://genome.ucsc.edu/FAQ/FAQformat.html#format1 ...
written 10 weeks ago by Martombo2.6k
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Comment: C: How to change my colnames(count.table) as exactly similar to my rownames(meta)?
... Please try and solve your R problems before posting questions on a specialized website like Biostars. You can generalize your problem like: "how to change rownames of a matrix" and google that. Otherwise you can try and understand the code you posted, if you didn't write it yourself, as you alread ...
written 4 months ago by Martombo2.6k
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Comment: C: Differential Expression Analysis with batches which have different biological gr
... How can you distinguish between batch effect noise and the biological variability you're interested in for batches 1 and 2? ...
written 4 months ago by Martombo2.6k
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Answer: C: Iteration to count the number of raw reads
... Yep, exactly. The second ` stops the expression at: `gunzip -c $f1 | echo $((` If you want to keep this line you can maybe use awk to divide by 4: RAW_READS=`gunzip -c $f1 | wc -l | awk '{print($1/4)}'` **edit**: this is probably more efficient: RAW_READS=`gunzip -c $f1 | awk 'END{ ...
written 5 months ago by Martombo2.6k

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Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 3 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Scholar 5 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Epic Question 10 months ago, created a question with more than 10,000 views. For Sjdboverhang Option In Star
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
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Popular Question 13 months ago, created a question with more than 1,000 views. For human Natural Antisense Transcript database
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 22 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Scholar 22 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 22 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.
Popular Question 23 months ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Scholar 2.0 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
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