User: Martombo

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Martombo2.1k
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Seville, ES
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Joined:
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Posts by Martombo

<prev • 259 results • page 1 of 26 • next >
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Comment: C: Download a list of DOI with Sci-hub
... look at these previous threads: https://www.biostars.org/p/47992/, https://www.biostars.org/p/45647/ ...
written 7 days ago by Martombo2.1k
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Comment: C: how to calculate the log FC for -1.5 fold change?
... So if log2FC = log2(FC), to get the FC you have to do FC = 2^log2(FC). So if your log2FC is -1.5 you have to compute 2^-1.5 ...
written 14 days ago by Martombo2.1k
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Comment: C: How to run Py-script 300 times with 3 new variables and a new output-file each t
... why would the constant arguments interfere with running a bash script? ...
written 7 weeks ago by Martombo2.1k
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Comment: C: RNA-Seq counts for all genes?
... After re-reading my old comment (somebody just left an upvote), I feel like one of the main point was not mentioned in this discussion: when analysing bulk RNA-seq we're often ignoring cell to cell differences, which can be a major source of variation. In a population of millions of cells there migh ...
written 8 weeks ago by Martombo2.1k
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Comment: C: Bioinformatics project manager for NGS center
... I would mention the fact that these are post-doc positions in the post, as it is an important property of the job. ...
written 8 weeks ago by Martombo2.1k
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Answer: C: Percentage of RNA-seq reads in exonic, intronic, intergenic and splice junction
... You can use read_distribution.py from RSeQC for this. It works with a bed format as input. ...
written 10 weeks ago by Martombo2.1k
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Answer: A: Mutation in one gene in TCGA data
... cBioPortal is most likely the easiest choice indeed. Cancers are classified by tissue of origin, so you'll find colorectal cancer under the "Bowel" section. Frameshift mutations are also typically included in the report. ...
written 12 weeks ago by Martombo2.1k
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Comment: C: Gene Co-expression analysis with less number of replicates
... I think the critical point here is not (only) the number of replicates, but rather the number of different condition / samples you have. Given that the original poster only had 3 different samples, I guess it was impossible in his case to build a gene co-expression network. With so few samples in fa ...
written 12 weeks ago by Martombo2.1k
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Comment: C: Why DE genes are not among highly variable genes between groups
... did you determine your "highly variable genes" as it is indicated in your first reference? If so, these are not highly variable genes between groups A and B, as you call them, but rather genes with the highest variance in your data. That means they can change a lot independently of the group. For th ...
written 3 months ago by Martombo2.1k
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Comment: C: Selection of hub gene on the basis of node degree
... I think the hub concept applies especially well to a protein-protein interaction network, where you have "sticky" proteins, ubiquitins, plymerases, histones, GNGs that are in some cases associated to a lot of other proteins. A co-expression network doesn't necessarily have hubs. 40 connections in pa ...
written 4 months ago by Martombo2.1k

Latest awards to Martombo

Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 6 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Scholar 6 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 7 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Popular Question 8 months ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 8 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Appreciated 13 months ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Great Question 15 months ago, created a question with more than 5,000 views. For Sjdboverhang Option In Star
Appreciated 17 months ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Popular Question 2.0 years ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Popular Question 2.3 years ago, created a question with more than 1,000 views. For misc_RNA in Ensembl
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 2.5 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 2.7 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.

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