User: Sentinel156

gravatar for Sentinel156
Sentinel156120
Reputation:
120
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Trusted
Location:
Melbourne, Australia
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3 days, 4 hours ago
Joined:
3 years, 2 months ago
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Posts by Sentinel156

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Validating ChIP-seq peak-calling output across replicates
... OP you could also use the excellent [Deeptools2][1] package to look at variation in your technical reps using the plotPCA/plotCorrelation functions [1]: https://deeptools.readthedocs.io/en/latest/ ...
written 2.4 years ago by Sentinel156120
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Comment: C: Validating ChIP-seq peak-calling output across replicates
... Nice! however how current is that ENCODE pipeline (your first link)? I've used the [main IDR repo][1] recently but was never quite sure how running IDR this way compares. Also how important is it to go through the process of generating and calling peaks from pseudoreplicates (as per the ENCODE pipel ...
written 2.4 years ago by Sentinel156120
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Answer: A: Extracting a set of complete genes from de novo assembled unannotated contigs
... I'm assuming you are working on a diploid eukaryote? How can you possibly determine whether there are two copies of each gene from a de novo assembly? Won't reads from either chromosome simply be collapsed into a single contig with the variant sites annotated at best? What assembler did you use for ...
written 2.4 years ago by Sentinel156120
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Answer: A: BioMart dataset for S pombe
... Hi, Did you find a solution to this? I was also having the same issue. There seems to be a problem pulling the metadata from the wrong host address as you say. I didn't want to waste time manually editing the `makeTxDbFromBiomart()` function so I made a TxDb from GFF3 file instead as follows: `li ...
written 2.4 years ago by Sentinel156120
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Answer: A: Get normalized count Data using DESeq2 in R
... Hi, this is pretty simple using DESeq2's counts function and has been asked many times before. See [here][1] and [here][2] for examples. [1]: https://www.biostars.org/p/162775/ [2]: https://www.biostars.org/p/149289/ ...
written 2.4 years ago by Sentinel156120
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Comment: C: Useful Bash Commands To Handle Fasta Files
... This is good but wont work for the odd fasta file where the sequence is wrapped onto a newline after a certain number of characters as some programs like to return. ...
written 2.5 years ago by Sentinel156120
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Answer: A: The Biostar Handbook. A bioinformatics e-book for beginners.
... I've been following this for the last couple of months and really glad to see it released! It was an instant buy for me as a wet-lab phd student interested in bioinformatics. I was wondering if it is possible to supply an epub version alongside mobi for those without kindle e-readers? Also is there ...
written 2.5 years ago by Sentinel156120
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quantification of PolII Ser-5 enrichment per gene
... Dear all, Perhaps a simple question but one I have not been able to find a consensus on. I have two biological replicates of active PolII (PolII Ser5) CHIP-seq data plus an INPUT replicate. I am trying to generate a single fold enrichment (or log2 ratio or similar) value for PolII per gene in my y ...
chip-seq written 2.5 years ago by Sentinel156120
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RNA-seq replicates pooled before sequencing. How to proceed with DGE analysis?
... I'm helping a colleague analyse RNA-seq data to find differentially expressed genes. There are 4 conditions with 3 biological replicates each and we are interested in all possible pairwise comparisons. Unfortunately they made a big mistake by pooling RNA from each of the three biological replicates ...
rna-seq written 3.2 years ago by Sentinel156120 • updated 3.2 years ago by Irsan6.9k
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DGE analysis using stranded and unstranded RNA-seq libraries.
... Hi all, I am working with Illumina HiSeq 2000 100bp single end RNA-seq data. Some of my samples originate from unstranded libraries and some from stranded libraries. I'm trying to understand the best way to do read summarisation for these libraries using featurecounts for eventual DGE analysis. To ...
rna-seq written 3.2 years ago by Sentinel156120 • updated 3.2 years ago by Devon Ryan90k

Latest awards to Sentinel156

Student 13 months ago, asked a question with at least 3 up-votes. For RNA-seq replicates pooled before sequencing. How to proceed with DGE analysis?
Popular Question 15 months ago, created a question with more than 1,000 views. For DGE analysis using stranded and unstranded RNA-seq libraries.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For RNA-seq replicates pooled before sequencing. How to proceed with DGE analysis?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Validating ChIP-seq peak-calling output across replicates
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Validating ChIP-seq peak-calling output across replicates

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