User: Alejandro Reyes

gravatar for Alejandro Reyes
Alejandro Reyes1.6k
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Location:
Dana-Farber Cancer Institute, Boston, USA
Twitter:
@areyesq
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Last seen:
1 week ago
Joined:
6 years, 9 months ago
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Posts by Alejandro Reyes

<prev • 273 results • page 1 of 28 • next >
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Answer: A: Kallisto output with DEXSeq
... Hi! I have not personally try something like that, but I know that others have use the kallisto output as input to DEXSeq. See for example these two papers from Mark Robinson's lab: 1. https://f1000research.com/articles/5-1356/v1 2. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-01 ...
written 5 weeks ago by Alejandro Reyes1.6k
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Answer: A: DEXSeq and DRIMSeq on paired samples?
... Hi zoe.ward,  For DEXSeq's vignette, this is documented in the section "4 Additional technical or experimental variables". Please let us know if something is not clear. Shortly, you need to pass the following formulae to both estimateDispersions and testForDEU: formulaFullModel = ~ sample + exon + ...
written 7 weeks ago by Alejandro Reyes1.6k
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Answer: A: Dexseq output interpretation
... Hi yelekley, I think the answers to these questions are in the section "2.4 Preparing the annotation" of the DEXSeq vignette. Did you already have a look at it? If something is unclear from this description please let us know and we will be happy to clarify it.  ...
written 3 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq analysis with large number of samples
... Yeah, the GLMs can take very long to fit when the models are large. One option is just to configure a BPPARAM with a cluster configuration and distribute it across many jobs. With such number of samples some of the steps from DEXSeq might not be needed. I would have a look at the diffSplice function ...
written 3 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... Thanks for the details. I could reproduce the error message using python 3.6 and HTSeq 0.10.0: I think it is a bug in HTSeq. I'll report this to the maintainers of HTSeq. While this gets fixed, I would recommend  using python 2.7.  Alejandro ps. just uploaded the resulting file here: https://www.d ...
written 4 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... I just ran the following without problems using python 2.7.10 and HTSeq 0.6.1p1: curl -o Homo_sapiens.GRCh37.87.gtf.gz ftp://ftp.ensembl.org/pub/grch37/update/gtf/homo_sapiens//Homo_sapiens.GRCh37.87.gtf.gz gunzip Homo_sapiens.GRCh37.87.gtf.gz python ~/Work/Rpcks/DEXSeq/inst/python_scripts/dexseq_p ...
written 4 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... Oh I see, sorry I did not catch that earlier. Could you point me to the link to the gtf file that you are using? ...
written 4 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... Hi Suzanne, have you checked if there are gene identifiers that appear in multiple chromosomes? ...
written 4 months ago by Alejandro Reyes1.6k
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Answer: A: DEXSeq: Error running dexseq_prepare_annotation.py
... Hi Suzanne,  The error message indicates that the same gene ID was found in two different chromosomes. As you suspect this is likely an error in the annotation file. The easiest solution is to remove that gene identifier from the gtf file.  Best regards, Alejandro ...
written 4 months ago by Alejandro Reyes1.6k
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Answer: A: DEXseq with technical replicates
... Hi g.e.novakowsky,  The DEXSeq model considers two sources of variation, (1) biological, which is estimated from biological replicates and (2) technical, which is small compared to biological variability, follows a Poisson distribution and can be estimated directly from the mean (see for example: h ...
written 4 months ago by Alejandro Reyes1.6k

Latest awards to Alejandro Reyes

Scholar 17 months ago, created an answer that has been accepted. For A: DEXSeqHTML and biomart object
Scholar 17 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Translating model formula from DESeq to DEXSeq
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: DEXSeq with mutliple experimental conditions - definig contrasts
Scholar 2.6 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.8 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: DEXSeq and Independent filtering
Scholar 3.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Centurion 3.8 years ago, created 100 posts.

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